The quality of unconventional volcanic reservoirs depends on dissolution spaces formed by diagenesis, yet their genesis and evolution are poorly understood. Here, we recover the formation and evolution processes of the dissolution pores using thin sections, reservoir porosity and permeability, major element analysis, electron probe microanalysis, in situ micro-scale carbon and oxygen stable isotopes, well logging, and seismic data. In the Palaeogene Shenhu Formation volcanic reservoir of the Huizhou Sag, Pearl River Mouth Basin (PRMB), dissolution pores dominate the reservoir space. During the epigenetic diagenetic stage, volcanic rocks underwent a prolonged weathering and dissolution (60.8-47.8 Ma), which increased the porosity. Primary pores were partially filled and damaged by first-phase quartz. During the burial diagenetic stage, secondary minerals, including chlorite, laumontite, second-phase quartz and calcite, filled the residual primary and weathering-dissolution pores. The diagenetic sequence of these minerals, combined with mineral thermometers and thermal history, indicates that chlorite formed at approximately 13-17 Ma and the subsequent laumontite were the primary causes of reservoir degradation. However, the extensive dissolution pores in chlorite aggregates and the volcanic matrix suggest post-filling dissolution by fluids, which formed the effective reservoir pores. The delta 13C (-4.296 parts per thousand to -11.987 parts per thousand) and delta 18O (-10.182 parts per thousand to -17.934 parts per thousand) values of calcite associated with dissolution pores indicate that the dissolution fluid was organic acid derived from the Wenchang Formation's hydrocarbon generation process. Temperature-driven transformation of secondary minerals may also provide some effective porosity, but organic acid-driven dissolution is likely the dominant mechanism for reservoir formation. A favourable relationship with source rocks is the necessary condition for forming promising reservoirs, and weathering unconformities and faults likely served as migration channels for organic acids. This study, by revealing the complexity of the formation process of dissolution-type volcanic reservoirs, provides important theoretical foundations and practical guidance for oil and gas exploration and development in other regions.

The genus Sinocyclocheilus represents the world's most diverse cavefish radiation, typically exhibiting troglomorphic traits such as scale regression and eye degeneration. Notably, Sinocyclocheilus macrolepis from a tributary of the Long-Jiang of the Pearl River retains fully developed scales despite inhabiting epigean streams, a rare trait among its cave-adapted congeners. The Sinocyclocheilus specimens collected from a tributary of the Hongshui-He of the Pearl River in South Guizhou exhibit overall similarities to S. macrolepis with fully developed scales and normal eyes. Phylogenetic analyses using mitochondrial Cyt b and ND4 genes reveal that these specimens represent a novel species, sister to S. macrolepis but with significant genetic divergence, and closely related to Sinocyclocheilus ronganensis. This new species was designated as Sinocyclocheilus pingchowensis in this study. Morphologically, S. pingchowensis differs from S. macrolepis in lateral-line scale counts, head width, gill-opening position and pelvic-fin ray counts. S. pingchowensis along with S. macrolepis and S. ronganensis are herein defined as the S. macrolepis group based on the shared synapomorphies and phylogenetic affinities. The phylogenetic tree suggests that the retention of scales in the species pair of S. pingchowensis and S. macrolepis represents a rare case of evolutionary reversal from cave-adapted degeneration. This phenotypic re-emergence correlates with their re-colonization of surface water, likely reflecting a synergistic adaptation to both photic exposure and occupation of the niche of mid-upper water strata, coinciding with relaxed selection on cave-associated trade-offs. The divergence of S. pingchowensis from its sister species was likely triggered by the river capture event between the two rivers.

Lepturichthys fimbriata is a small benthic fish inhabiting rapid rocky shoals within the Jinsha River system. This species holds considerable significance for studying animal morphology, ecology, and evolution due to its specialized habitat adaptations. We generated the first chromosome-level genome assembly of L. fimbriata through integrated HiFi, Illumina, and Hi-C sequencing. The 591 Mb genome features a scaffold N50 of 20.9 Mb, with 94.2% (556.18 Mb) of sequences anchored to 25 pseudo-chromosomes (2n = 50). Genome annotation identified 36.01% (212.72 Mb) repetitive elements and 21,320 protein-coding genes, with assembly completeness evidenced by a 97.3% BUSCO score. This high-quality genome provides a crucial resource for investigating L. fimbriata genetic diversity and ecological adaptation mechanisms.

The first complete mitochondrial genome of Ptychidio longibarbus is reported here. The circular genome is 16,604 bp long, containing 13 protein-coding genes, 22 tRNAs, two rRNAs, and a control region, with ∼239× coverage. All genes are located on the heavy strand except nad6 and eight tRNAs on the light strand. The mitogenome shows a typical A+T bias (57.72%). Phylogenetic analysis based on 12 concatenated PCGs places P. longibarbus in a well-supported clade with P. jordani and P. macrops, confirming its taxonomic position and providing new genomic resources for Labeoninae systematics and conservation.

Understanding the genetic basis of phenotypic diversity is fundamental to evolutionary biology and selective breeding. The White Cloud Mountain minnow (Tanichthys albonubes) is a renowned ornamental fish, yet the genomic basis of its prized ornamental traits (e.g., golden body color and long-fin) remains poorly understood. Here, we present a high-quality chromosome-level genome assembly for T. albonubes, which has a size of 1067.12 Mb with contig and scaffold N50 values of 5.65 Mb and 41.71 Mb, respectively. A total of 1036.50 Mb (97.13%) was anchored into 25 pseudo-chromosomes. The genome is highly repetitive (53.48% repetitive sequences) and encodes 24 121 protein-coding genes. Based on this reference genome and whole genome resequencing data of 126 individuals from four populations (one wild population, one native hatchery population, golden strain and long-fin strain), we revealed that the golden strain originated directly from the native hatchery stock, while the long-fin strain was derived from a distinct wild lineage. By integrating window-based pairwise F ST scans with GWAS analysis, we demonstrated that the golden body color is a monogenic trait, with chrna2b on chromosome 15 as a prime candidate. In contrast, we found fin elongation is a polygenic trait and identified four candidate genes (mosmob, tbx18, vwa8, wnt6b) and the hedgehog signaling pathway underpinned this long-fin phenotype. Our study provides fundamental genomic resources and unveils the genetic architecture underlying two striking ornamental traits of T. albonubes, offering crucial insights for its further selective breeding and conservation.

The gold barb (Barbodes semifasciolatus), a member of the Cyprinidae family, exhibits remarkable adaptability to highly acidic environments, making it an ideal model for studying extreme environmental adaptation. However, its genome has not been previously characterized. To address this, we assembled a high-quality chromosome-scale genome for B. semifasciolatus using High-Fidelity (HiFi) sequencing and Hi-C technology. The resulting haplotype-resolved assemblies, spanning 776 Mb and 779 Mb across 25 chromosomes, achieved genome coverages of 99.5% and 99.7%, respectively, and included four gap-free chromosomes. Genome quality assessment using BUSCO indicated a high completeness score of 98.2% for haplotype1 and 98.3% for haplotype2, further validated by strong synteny with the zebrafish (Danio rerio), confirming the assembly’s integrity and continuity. Through integration of full-length transcriptome data, RNA sequencing, and homology-based annotation, we identified 26,057 protein-coding genes with 2,087 pseudogenes in haplotype 2, and 25,622 protein-coding genes with 2,101 pseudogenes in haplotype 1. This high-resolution genome assembly is a crucial resource for advancing research in the Cyprinidae, particularly for understanding adaptive evolution in extreme environments.

The South China region, with its complex river system and mountains, served as a key Pleistocene refugium. We investigated the impact of historical climate fluctuations and geographical isolation on the genetic diversity of freshwater species in South China using Pterocryptis cochinchinensis as an exemplar. Two mitochondrial and two nuclear gene markers from 331 individuals across 14 populations were employed. Phylogenetic trees based on mtDNA loci confirmed three distinct lineages, whereas phylogenetic trees using 2 nuclear DNA loci did not obtain the signal of lineage division. Genetic diversity and differentiation indicated that P. cochinchinensis possesses significant genetic diversity, with variation among populations being the primary source of the total variation. SAMOVA supported two groups: one group comprising the Dongjiang and Beijiang River basins, and the other group including the basins of other rivers. The divergence time estimated between the two groups was 4.62 million years ago, which could be linked to the swift uplift of the Tibetan Plateau. Star-like network, EBSP analysis, and neutrality tests indicated the populations remained stable over a long period. Furthermore, the Wuyi Mountains and Nanling Mountains appear to serve as refuges for P. cochinchinensis populations. Geographic features such as the Qiongzhou Strait and Yinggeling Mountains may obstruct the expansion of P. cochinchinensis. These findings deepen our understanding of P. cochinchinensis' evolution and population structure, aiding conservation efforts.

Stratigraphic stacking patterns in marginal marine environments are strongly influenced by shoreline migration, which governs the development of key sequence surfaces, system tracts, and reservoir quality sand bodies. This paper aims to characterize the evolution of shoreline trajectories during the Early to Middle Miocene in the Huizhou Sag of the Pearl River Mouth Basin and to assess their influence on the development of lithologic sand bodies. We integrated high-resolution 3D seismic interpretation with well-log and sedimentological data to identify clinoform geometries and classify shoreline trajectories. Transitions between trajectory types were used to delineate sequence stratigraphic surfaces, and seismic geomorphologic analysis was applied to characterize the morphology and distribution of associated strip sand bodies. Two types of clinoforms and four primary shoreline trajectory styles have been identified: descending regressive, ascending regressive (concave up), retreating transgressive, and ascending regressive (convex up). Whereas descending regressive trajectories coincide with sequence boundaries, the transition from concave up to transgressive marks the maximum regressive surface. The shift from a retreating transgressive to a convex-up regressive trajectory defines the maximum flooding surface. Seismic sedimentological analysis reveals a strong genetic relationship between shoreline trajectories and sand body types. Whereas beach ridge sand bodies are associated with descending regressive trajectories, barrier bar systems correspond to retreating transgressive ones. Shoreline trajectory analysis supports the construction of high-resolution sequence stratigraphic frameworks and enables predictive mapping of lithologic traps. This approach enhances the understanding of sedimentary processes in deltaic and marginal marine systems, providing practical value for hydrocarbon exploration targeting stratigraphic reservoirs.

Preserving healthy river habitats is essential for maintaining fish diversity. Over time, anthropogenic activities have severely damaged river habitats, leading to notable changes in fish diversity patterns. Conducting thorough and reliable investigations into fish diversity is crucial for assessing anthropogenic impacts on diversity. In August 2023, a water ecology survey was conducted across 20 terraced river sections in the mainstem of the Jialing River, resulting in the collection of 60 environmental DNA water samples. The survey identified 99 fish species, representing 74 genera across 7 orders and 20 families, with the Cyprinidae exhibiting the highest number of species. The fish communities are predominantly composed of species inhabiting slow flowing water, demersal fish, omnivores, and fish spawning adhesive eggs. Overall, small-bodied fish dominate the mainstem of the Jialing River, and the species preferring flowing habitats are relatively scarce. In addition, geographic division analyses revealed minimal variations in fish species composition and diversity among the terraced reservoirs and across the upper, middle, and lower reaches. Notably, the fish compositions in the middle and lower reaches were found to be similar, indicating a certain degree of convergence in these sections of the Jialing River. In conclusion, this study unveils the current status and distribution pattern of fish diversity in the Jialing River and highlights the extent of anthropogenic activities’ impact on fish diversity.

To investigate the species composition, reproductive dynamics, and hydrological drivers of fish resources in the early stage in the Guiping section of the Xunjiang River, we conducted a two-year survey (2022–2023) downstream of the Datengxia Dam. A total of 22,464 fish eggs and larvae were collected, representing 6 orders, 17 families, and 67 species, with Cyprinidae (58.2%) as the dominant family. Dominant species included Squaliobarbus curriculus, Gobiidae, Hemiculter leucisculus, and Culter, exhibiting significant interannual variation in abundance. The breeding season peaked from May to September, accounting for 94.6% of annual recruitment. Hydrological conditions strongly influenced reproductive output: the multiple flood pulse periods in 2022 (peak discharge: 29,000 m3/s) yielded 34.997 billion eggs and larvae, whereas reduced flows in 2023 (peak discharge: 12,200 m3/s) led to a 75.4% decline (8.620 billion). Redundancy analysis (RDA) revealed that discharge, water temperature, natural hydrological data, and dissolved oxygen were the primary environmental drivers, explaining 46.11% of variability in larval abundance (p < 0.001). Notably, the proportion of important economic fish, “four major Chinese carps”, plummeted from 4.9% (2022) to less than 0.1% (2023), indicating spawning ground function degradation. Our results demonstrate that flood pulses are essential for sustaining fish recruitment, particularly for pelagic spawning riverine fish like the four major Chinese carps. Their proportion plummeted to less than 0.1% in 2023, highlighting the urgent need for eco-hydrological management in the Xunjiang River.

The order Siluriformes, a hyperdiverse teleost clade with over 3,000 species, exemplifies adaptive radiation through significant phenotypic innovations such as aerial respiration. However, the limited availability of high-quality genomes, particularly in underrepresented families such as Sisoridae, has hindered phylogenomic and mechanistic studies of their ecological diversification. Here, we present a nearly complete telomere-to-telomere (T2T) genome assembly of Bagarius rutilus (Banded Goonch) generated by a hybrid sequencing approach integrating PacBio HiFi, Oxford Nanopore ultra-long and Hi-C technologies. The 618.3 Mb genome (contig N50 = 21.06 Mb, scaffold N50 = 25.46 Mb) was resolved into 26 chromosomes, achieving a genome coverage of 98.17%. The quality of the assembly was validated by a BUSCO score of 97.5% (Actinopterygii_odb10) and high conservation of synteny with other catfish species. Based on RNA sequencing, homology-based and de novo annotation, we identified 29,106 protein-coding genes. This chromosome-level genome represents one of the highest quality Siluriformes assemblies to date and provides a critical resource for reconstructing adaptive landscapes and exploring the genetic basis of phenotypic innovation in catfish.

The Yuanjiang River, situated in the upper reaches of the Red River, is a crucial component of a biodiversity hotspot in the mountains of southwestern China, supporting a high diversity of fish species. Nevertheless, systematic research on fish diversity in the Yuanjiang River is scarce, scattered, and outdated. In our study, we produced 764 DNA barcodes belonging to 64 fish morphospecies to evaluate fish diversity in the Yuanjiang River. Barcoding gap analysis and DNA-based delimitation approaches achieved a high identification success rate (>93%), indicating that DNA barcoding is a practical approach for delimiting fish in the Yuanjiang River. However, four species were characterized by high levels of intraspecific divergence, generating multiple clades and/or molecular operational taxonomic units (MOTUs), suggesting that these species might comprise undetected species. Meanwhile, two closely related species within the genus Schistura, i.e., S. callichroma and S. caudofurca, cannot be delimited by the DNA barcoding technique, which is indicative of recent speciation. In summary, this study established a reliable DNA barcode reference library for fish species in the Yuanjiang River and revealed previously unknown fish diversity.

Hongiastoma zhangbuensis sp. nov. is described from a tributary of the upper reach of the Pearl River basin based on the morphological and molecular data. It is distinguished from all known species within the subfamily Acrossocheilinae by having a combination of the following characteristics: a crescent horny sheath on the lower jaw, a less prominent lower lip limited to the corners of the mouth, a serrated posterior edge of the last simple dorsal-ray, 47–50 lateral-line scales, 9 scales above the lateral line, 16–18 circumpeduncular scales, and 16–18 pre-dorsal midline scales. The molecular phylogeny revealed that H. zhangbuensis sp. nov. was a sister taxon to Hongiastomata argentatum, with a genetic distance ranging from 10.49% to 10.68%. Together, they formed a lineage at the base of the Acrossocheilinae clade. Furthermore, the interspecific genetic distances between the new species and those of Onychostoma sensu lato ranged from 9.9 to 13.4%, indicating significant genetic divergence between this new species and all known species within Onychostoma sensu lato. Therefore, both morphological and molecular data support the recognition of this species as new.

Understanding the mechanisms that promote coexistence between functionally analogous non-native and native species that share similar prey is important for predicting the ecological consequences of their competitive interactions. Theory predicts that species coexistence is facilitated by stabilizing mechanisms that enhance inter-specific trophic niche partitioning, and/ or the equalizing mechanisms that reduce differences in the average fitness. Inter-specific niche partitioning, influenced by the ecological opportunity in prey resources, also affects intra-specific niche partitioning and individual niche expansion. These theories were tested using the non-native mrigal carp Cirrhinus mrigala and its congener native mud carp C. molitorella that coexist across the Pearl River basin, Southern China, with their trophic interactions analysed using DNA metabarcoding on fish gut contents sampled across the basin in both the dry and wet seasons of 2019 and 2021. The results revealed that the inter-specific trophic niche overlap was lower than their intra-specific trophic niche overlap, suggesting their coexistence was supported by stabilizing mechanisms. The ecological opportunity in prey resources was driving inter-specific niche partitioning and this partitioning then positively influenced intra-specific niche partitioning and individual niche expansion, especially in mrigal carp that had larger body sizes and occupied higher trophic positions at constricted individual niches. Fish body size also affected inter-specific niche partitioning and the relationship between inter- and intra-specific niche partitioning, with positive effects on both in mrigal carp but negative effects on both in mud carp. The results thus provide a mechanistic explanation on how closely related non-native and native species coexist and highlight the importance of dietary plasticity in facilitating the invasion of non-native species.

Whole-genome duplication (WGD), or polyploidization, is a major contributor to biodiversity. However, the establishment and survival of WGDs are often considered to be stochastic, since elucidating the processes of WGD establishment remains challenging. In the current study, we explored the processes leading to polyploidy establishment in snow carp (Cyprinidae: Schizothoracinae), a predominant component of the ichthyofauna of the Tibetan Plateau and its surrounding areas. Using large-scale genomic data from isoform sequencing, we analyzed ohnolog genealogies and divergence in hundreds to thousands of gene families across major snow carp lineages. Our findings demonstrated that independent autopolyploidization subsequent to speciation was prevalent, while autopolyploidization followed by speciation also occurred in the diversification of snow carp. This was further supported by matrilineal divergence and drainage evolution evidence. Contrary to the long-standing hypothesis that ancient polyploidization preceded the diversification of snow carp, we determined that polyploidy in extant snow carp was established by recurrent autopolyploidization events during the Pleistocene. These findings indicate that the diversification of extant snow carp resembles a coordinated duet: first, the uplift of the Tibetan Plateau orchestrated the biogeography and diversification of their diploid progenitors; then, the extensive Pliocene-Pleistocene climate changes acted as relay runners, further fueling diversification through recurrent autopolyploidization. Overall, this study not only reveals a hitherto unrecognized recent WGD lineage in vertebrates but also advances current understanding of WGD processes, emphasizing that WGD establishment is a nonstochastic event, emerging from numerous adaptations to environmental challenges and recurring throughout evolutionary history rather than merely in plants.

Mixed siliciclastic-carbonate systems are regulated interactively by factors such as siliciclastic sediment supply, carbonate production, sea-level change, tectonism, and climate conditions. These systems record vital information that aids in understanding ancient environments. This study used a merged 3D seismic volume, in conjunction with over 100 industrial wells, to systematically investigate the stratigraphic-sedimentary evolution of such a system within the Huizhou Sag of the Pearl River Mouth Basin, located on the northern continental shelf of the South China Sea. In total, six major sequence boundaries were identified for the Zhujiang Formation within the area, thus subdividing the interval into five typical third-order depositional sequences. Each of these sequences can be divided into a transgressive and a highstand systems tract. Lowstand or falling stage systems tracts were also recognized, the deposition of which was potentially in response to the uplifting process of the Dongsha Rise. During the deposition of the Zhujiang Formation, the Huizhou Sag may have undergone a sequential evolutionary history from delta-shore, to delta-shore-tidal-lagoon, to delta-shore-carbonate, and finally to delta-shore-shallow marine systems. This evolution responded to a varying degree of mixing processes, which was mainly regulated by siliciclastic sediment supply, confined paleomorphology, and local oceanic currents. Furthermore, the deposition of the Zhujiang Formation in the Huizhou Area was time-equivalent with the spreading process after the ridge jump of the South China Sea (23–16.5 Ma), providing valuable insights into sea-level fluctuations, provenance changes, and tectonic evolution. Our results may also shed light on the evaluation of lithologic traps and hydrocarbon sweet spots within mixed siliciclastic-carbonate systems.

The genus Silurus, an important group of catfish, exhibits heterogeneous distribution in Eurasian freshwater systems. This group includes economically important and endangered species, thereby attracting considerable scientific interest. Despite this interest, the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus. Herein, we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes (mitogenomes) from 13 morphological species to reconstruct the phylogenetic relationships, biogeographic history, and species diversity of Silurus. Our phylogenetic reconstructions identified eight clades, supported by both maximum-likelihood and Bayesian inference. Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units (MOTUs) in several taxa, including the Silurus asotus complex (four MOTUs) and Silurus microdorsalis (two MOTUs), suggesting that species diversity is underestimated in the genus. A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago (Ma), with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma, and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma. Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula, with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma. Key factors such as the Eocene-Oligocene extinction event, onset and intensification of the monsoon system, and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus.

AbstractFish dietary niche is a core focus, and it reflects the diversity of resources, habitats, or environments occupied by a species. However, whether geographic segregation among different populations triggers dietary diversification and concomitant fish niche shift remains unknown. In the present study, we selected the Black Amur bream (Megalobrama terminalis) is a migratory fish species that plays an important role in the material transfer and energy cycling of river ecosystems, inhabiting southern China drainage with multiple geographic populations. Here, we utilized the combined analyses of 18S rDNA high‐throughput sequencing in fish gut contents and fatty acid (FA) in muscle tissues to evaluate potential spatial patterns of habitat and resource use forM. terminalisin three rivers of southern China. Our results showed that prey items of the Xijiang (XR) population (Pearl River) exhibited the highest species diversity and richness among the three geographic populations. Moreover, diet composition ofM. terminaliswas affected by spatial differences associated with geographic segregation. Analyses of FA biomarkers indicated that the highest levels of C16:0, C18:3n‐3, and C18:2n‐6c were found in Wanquan (WS) population (Wanquan River). The XR population exhibited a distinct FA profile characterized by higher amounts of arachidonic acid (ARA) and docosahexaenoic acid (DHA). The Moyang (MY) population (Moyang River) acted as the linkage between WS and XR populations and consisted of middle levels of saturated FAs (SFAs) and polyunsaturated FAs (PUFAs). The XR population displayed a greater FA niche width compared with WS population. Furthermore, we observed a close positive relationship between the niche width and α‐diversity indices of dietary resources for FA proflies. Our study provides valued information to develop different conservation strategies among different populations and improve fisheries management forM. terminalisand other endemic species in local rivers.

Dam construction in riverine ecosystems has fragmented natural aquatic habitats and has altered environmental conditions. As a result, damming has been demonstrated to threaten aquatic biodiversity by reducing species distribution ranges and hindering gene exchange, leading to the inability to adapt to environmental changes. Knowledge of the contemporary genetic diversity and genetic structure of fish populations that are separated by dams is vital to developing effective conservation strategies, particularly for endangered fish species. We chose the Lianjiang River, a tributary of the Pearl River, as a case study to assess the effects of dams on the genetic diversity and genetic structure of an endangered fish species, Hemibagrus guttatus, using whole-genome resequencing data from 63 fish samples. The results indicated low levels of genetic diversity, high levels of inbreeding and decreasing trend of effective population size in fragmented H. guttatus populations. In addition, there were significant genetic structure and genetic differentiation among populations, suggesting that the dams might have affected H. guttatus populations. Our findings may benefit management and conservation practices for this endangered species that is currently suffering from the effects of dam construction.

The temperature changes in the middle-late Eocene had a profound impact on various ecosystems around the world. This has been confirmed not only in marine sediments but also in lake ecosystems, which have provided more detailed isochronous continental sedimentary records. Based on systematic palynological and element analyses of fine-grained lacustrine sediments from the Xijiang main subsag in the Pearl River Mouth Basin, southern China, we reconstructed the climate evolution of the middle-late Eocene. A total of 73 genera and 115 species of sporopollen fossils were identified from the middle-late Eocene in the study area. Three pollen zones comprising Quercoidites–Polypodiaceaesporites–Pinuspollenites, Pinuspollenites–Ulmipollenites–Cedripites, and Pinuspollenites–Abietineaepollenites–Juglanspollenites were established from bottom to top. The analysis of the vegetation types, climatic zones, and dry–humid types of the sporopollen showed that, in the study area, the Eocene was dominated by a subtropical–warm temperate climate: the early-late Eocene was dominated by a temperate climate, and the late Eocene was characterized by the prevalence of a warm temperate climate, which was consistent with the palaeoclimate reconstruction results for element geochemical indices (Fe/Mn, Sr/Cu, CIA, PIA, etc.). In addition, the comparative study showed that the middle-late Eocene in the study area was characterized by a warm and humid climate, which transitioned to a warm and cool semihumid–semiarid climate and then a warm and cool semihumid climate. These findings demonstrated a good coupling relationship with the trend for the changes in the global palaeotemperature and can be used as an isochronous continental sedimentary response.