Quiver trees ( Aloidendron dichotomum ) are large iconic succulent plants found in arid areas of southern Africa. These trees have been observed suffering from die-back symptoms for many years. Various environmental and abiotic factors have been investigated as possible causes of the symptoms. However, biotic causes, especially microfungi that commonly cause die-backs in trees, have never been considered. During a routine disease survey, symptomatic stems and roots of the dying trees were collected in the Cape Province, South Africa. Isolations were made from tissues at the leading edges of the lesions on symptomatic stems and roots, and the resulting fungi were identified using morphological characteristics and DNA sequence data of four loci (LSU, SSU, ITS and β-tubulin). Five species were identified: Paecilomyces formosus , Phaeoacremonium ( Pm. ) parasiticum , Pm. luteum , Xylogone sphaerospora , and the newly described Coniophoma aloidendri gen. et sp. nov . Three species, Pm. parasiticum and C. aloidendri from this study and Alanphillipsia ( Ala. ) aloes were tested for their pathogenicity on A. dichotomum plants in a greenhouse trial. All three species gave rise to lesions significantly different in size from the controls. The Pm. parasiticum strains showed larger necrotic lesions than C. aloidendri and Ala. aloes . However, none of the isolated fungi were aggressive or are known as primary pathogens, and the cause of the die-back on symptomatic trees remains to be determined.

The globally important plant pathogen Phytophthora cinnamomi was first reported in South Africa in 1931, where it caused substantial damage to avocado orchards. Surprisingly, 40 years passed before the pathogen was recognised as a significant threat to South Africa’s natural ecosystems. This first became evident when P. cinnamomi caused a “quick decline” of the iconic silver trees (Leucadendron argenteum) in the Cape Floristic Region (CFR) of the Western Cape Province. Subsequent research has underscored the role of P. cinnamomi as a major root rot pathogen affecting numerous native species. Despite these findings, there has been limited research on the extent of the threat P. cinnamomi poses to Cape flora, leaving the risk of extinction for many species largely unknown. A recent observation of P. cinnamomi causing rapid mortality in Sorocephalus imbricatus, a Critically Endangered Proteaceae, underscores the urgent need for a comprehensive evaluation of this pathogen’s impact on Cape flora and the associated extinction risks. Given the high number of rare and threatened species in the CFR, many of which belong to families known to be vulnerable to P. cinnamomi, there is a pressing need to initiate an intensive local research programme to fill this critical gap. To address this, we propose a structured research programme that will guide targeted mitigation efforts against P. cinnamomi. Enhancing our understanding of P. cinnamomi’s threat to the CFR, a global biodiversity hotspot, will be essential to inform conservation strategies and to set restoration priorities in the region.

The genus Phytophthora contains many destructive and globally important plant pathogens. In the last decade, targeted sampling efforts have resulted in a dramatic increase in the number of known species, as well as a better understanding of their global distribution. Routine activities undertaken in botanical gardens, combined with great numbers of local and international visitors, place botanical gardens at risk to the accidental introduction and establishment of pathogens such as Phytophthora spp. In this study, the occurrence of Phytophthora was investigated in two botanical gardens in the KwaZulu-Natal Province of South Africa. Symptomatic collar and stem tissues were collected, and root and rhizosphere soil samples were taken from trees exhibiting symptoms of decline. Standard baiting techniques and direct plating of symptomatic tissues revealed the presence of seven species of Phytophthora residing in four phylogenetic clades. Five of these species, P. cinnamomi, P. citrophthora, P. multivora, P. parvispora and the informally designated taxon Phytophthora sp. stellaris were known to be present in South Africa and P. aquimorbida was recorded for the first time. Of these, P. citrophthora represented a novel host-pathogen association causing bleeding cankers on indigenous Celtis africana. A multilocus phylogenetic analysis based on ITS, βtub, cox1 and hsp90 sequences showed the presence of an undescribed species belonging to the Phytophthora ITS Clade 5. This species is described here as Phytophthora mammiformis sp. nov. This study highlights the importance of monitoring botanical gardens for the detection and discovery of pathogens and emphasises their value as sites for the discovery of novel host-pathogen associations. Citation: Paap T, Balocchi F, Burgess TI, Bose T, Wingfield MJ (2024). A diverse range of Phytophthora species from botanical gardens in South Africa, including the novel Clade 5 species, Phytophthora mammiformis sp. nov. Fungal Systematics and Evolution 13: 111-122. doi: 10.3114/fuse.2024.13.05.

Widdringtonia is a genus of native southern African Cupressaceae trees comprising two species that occur in the mountains of the Western Cape province, South Africa. Widdringtonia cedarbergensis has a localised distribution and is critically endangered, while W. nodiflora is widespread and common. Little is known regarding the biotic associations of these trees. The aim of this study was, consequently, to identify bark beetles (Curculionidae: Scolytinae) and their associated fungi on Widdringtonia species in the Western Cape. Bark beetles were collected from infested W. cedarbergensis at three different locations in the Cederberg and from W. nodiflora at one site on the Franschhoek Pass. Beetle identification was based on morphology and sequence data of the COI gene region. Fungi were isolated from beetles, their frass and the walls of their tunnels and grouped according to morphology. Morphogroups were identified by sequencing the ITS region of representative isolates. Four phylogenetically closely related bark beetle species residing in the genus Lanurgus (Micracidini) were identified, three from W. cedarbergensis stem sections, twigs and cones, respectively, and one from W. nodiflora stems. Of these, only the W. cedarbergensis twig beetle is of a previously described species and is currently known as Diplotrichus widdringtoniae. Piskurozyma sp. (Tremellomycetes) and Yamadazyma sp. (Saccharomycetes) yeasts were most closely associated with D. widdringtoniae (Lanurgus sp. 1) and Lanurgus sp. 2 beetles, whereas Geosmithia spp. (Sordariomycetes) had a strong association with Lanurgus sp. 3 and Lanurgus sp. 4. This is the first comprehensive report of bark beetles and their associated fungi infesting Widdringtonia.

Ambrosia beetles (Coleoptera: Curculionidae: Scolytinae) are small wood-boring insects that live in an obligate symbiosis with fungi, which serve as their primary food source. Beetles residing in the genus Euwallacea have evolved a unique association with a clade of Fusarium that falls within the aptly named Ambrosia Fusarium Clade (AFC). The discovery of the invasive polyphagous shot hole borer, E. fornicatus, in South Africa, has heightened awareness of ambrosia beetles and their symbionts in the country. In this study, we investigated the Fusarium symbionts of three species of Euwallacea in South Africa, with a specific focus on those associated with E. xanthopus. Isolations of Fusarium strains from both living and dissected beetles yielded nearly 100 isolates. Using multigene phylogenetic analyses, these isolates were identified as six different Fusarium species. Fusarium hypothenemi and F. euwallaceae have previously been reported from South Africa. Fusarium pseudensiforme and Fusarium AF-6 are new records for the country. The remaining two species are new to science and are described here as F. rufum sp. nov. and F. floriferum sp. nov. Targeted fungal isolation from specific beetle body parts revealed that the AFC species collected were typically associated with the dissected beetle heads and helped us identify the likely nutritional symbiont of E. xanthopus. This study highlights the understudied diversity of fungal associates of ambrosia beetles present in South Africa.

Ralstonia solanacearum and R. pseudosolanacearum are well-known bacterial plant pathogens that cause significant losses to both ornamental and agricultural plants. It has been suggested that they are not the primary cause of bacterial wilt in Eucalyptus species, but rather are opportunistic, taking advantage of trees predisposed to infection by abiotic and biotic factors. To test this hypothesis, the bacterial community within the vascular tissue of asymptomatic Eucalyptus grandis x E. urophylla trees, and those displaying varying stages of infection in China and Indonesia were compared using 16S rRNA profiling. Asymptomatic trees growing in areas where bacterial infections had never previously been reported to occur were included as controls. Ralstonia species were found within the vascular tissue of both asymptomatic and symptomatic trees, in high abundance. In the control samples, bacterial diversity within the vascular tissue was high with a low abundance of Ralstonia species. The presence of Ralstonia species in asymptomatic and control samples supports the hypothesis that these species are latent and/or opportunistic pathogens in E. grandis x E. urophylla trees.

Cypress canker is an important fungal disease caused by at least seven different Seiridium species. The disease has been known on Cupressaceae trees in South Africa since the 1980’s, but its relevance was recently accentuated with an outbreak on native Widdringtonia nodiflora trees in the Western Cape. The causal agent, S. neocupressi, was previously unknown in the country, highlighting a lack of information regarding the disease in South Africa. The aim of this study was to investigate the occurrence of cypress canker and its causal agents across the country by sampling diseased Cupressaceae trees and reconsidering the identity of Seiridium strains previously collected in the country. Phylogenetic analyses revealed five known cypress canker pathogens and two putatively novel species. Seiridium cardinale was the most frequently isolated species in the Western Cape. Only two isolates of S. neocupressi were found outside the outbreak on Widdringtonia. Seiridium unicorne was most frequently isolated in the Gauteng and Free State provinces. Seiridium cancrinum, S. kenyanum and the two undescribed species were each recovered only in localised areas. Stem inoculations on x Hesperotropsis leylandii using S. cardinale, S. neocupressi and S. unicorne strains confirmed the pathogenicity of S. cardinale and S. neocupressi. In contrast, S. unicorne strains exhibited variable levels of aggressiveness. This study represents the first extensive consideration of cypress canker in South Africa and one of few studies on this important disease in the Southern Hemisphere.

Calonectria leaf blight caused by Calonectria spp. is among the most serious diseases affecting the health and sustainability of Eucalyptus plantations in southern China. Recent outbreaks of this disease in GuangDong Province prompted a need to identify the species involved. Typical symptoms of Calonectria leaf blight were observed on 2-year-old Eucalyptus urophylla × E. grandis trees in a plantation in the ZhaoQing region. In total, 38 Calonectria isolates were collected from 32 diseased trees. All isolates were identified using DNA sequence analyses of the translation elongation factor 1-α (tef1), β-tubulin (tub2), calmodulin (cmdA), and histone H3 (his3) gene regions. Phylogenetic analyses revealed that Calonectria queenslandica was the dominant species, accounting for 81.6% of the isolates collected. Other species isolated included C. pseudoreteaudii (10.5%), C. reteaudii (5.3%), and C. aconidialis (2.6%). This is the first report of C. queenslandica in China and all isolates had identical sequences in all four gene regions. PCR amplification using primers targeting the MAT1-1-1 and MAT1-2-1 genes in all C. queenslandica isolates revealed that only the MAT1-2 idiomorph was present. The results suggest that C. queenslandica was introduced into the sampled area with very limited genetic diversity. Pathogenicity tests were conducted on two Eucalyptus genotypes widely planted in the GuangDong Province using isolates representing all species collected. The results showed that these species could all cause disease but the predominance of C. queenslandica on infected trees suggests that it is the major driver of the disease problem studied. Different Eucalyptus genotypes used in the pathogenicity tests differed in susceptibility to infection by the Calonectria spp. tested, providing opportunities to avoid leaf blight by deploying disease-tolerant planting stock.

The pine pitch canker pathogen Fusarium circinatum is endemic in the southeastern United States and Central America and represents an invasive threat globally. This ecologically adaptable fungus readily infects all parts of its pine hosts, leading to widespread mortality of nursery seedlings and decline in the health and productivity of forest stands. Because trees infected by F. circinatum can remain asymptomatic for long periods of time, accurate and rapid tools are needed for real-time diagnostics and surveillance at ports, in nurseries, and in plantations. To meet this need and to limit the spread and impact of the pathogen, we developed a molecular test using loop-mediated isothermal amplification (LAMP), a technology that allows for the rapid detection of pathogen DNA on portable, field-capable devices. LAMP primers were designed and validated to amplify a gene region unique to F. circinatum. Using a globally representative collection of F. circinatum isolates and other closely related species, we have demonstrated that the assay can be used to identify F. circinatum across its genetic diversity and that it is sensitive to as few as 10 cells from purified DNA extracts. The assay can also be used with a simple, pipette-free DNA extraction method and is compatible with testing symptomatic pine tissues in the field. This assay has the potential to facilitate diagnostic and surveillance efforts both in the laboratory and in the field and, thus, to reduce the spread and impact of pitch canker worldwide.

Background: Sorocephalus imbricatus (Thunb.) R.Br. is a range-restricted species endemic to the Cape Floristic Region (CFR), South Africa. It is currently classified as Critically Endangered in accordance with the IUCN criteria. Like many other species endemic to the CFR, S. imbricatus is subjected to several major threats including habitat loss, habitat degradation and the impacts of invasive alien species. Sorocephalus imbricatus was recently identified as a species requiring improved representation in ex-situ collections. During field work undertaken to collect germ­plasm for this purpose, a concerning number of dead and dying plants were observed. Objectives: To determine the cause of rapid death of individuals in a remnant subpopulation of S. imbricatus. Method: A field visit to a subpopulation of the only extant population, Elands­kloof, was conducted to examine the symptoms associated with S. imbricatus mortality, and to collect samples for isolation and identification of putative pathogens. Results: Dead and dying plants showed clear symptoms of root and collar rot, with Phytophthora cinnamomi Rands recovered from all samples. The collections highlighted the severe impact of P. cinnamomi on S. imbricatus, with the size of the subpopulation being reduced from 62 to 37 individuals (a 40% reduction) between October 2021 and May 2022. Conclusion: This study describes, for the first time, rapid mortality of the Critically Endangered Proteaceae species, S. imbricatus, likely caused by the invasive pathogen P. cinnamomi. This concerning discovery highlights the urgent need for greater recognition of the threat P. cinnamomi poses not only to S. imbricatus, but to the broader floristic diversity of the CFR. Importantly, it illustrates a need for a substantial body of work to be undertaken to address a significant lack of knowledge regarding the relative threat that P. cinnamomi poses to species of the CFR.

Euphorbia mauritanica is a succulent shrub that is indigenous to South Africa and widely distributed throughout the country. Dying plants have been observed in their natural habitat in the Northern and Western Cape Provinces of South Africa in recent years. Stems displaying lesions were collected and the emerging cultures were identified based on ITS, LSU, ACT , RPB2 , TEF1 and/or TUB2 sequence data. Four filamentous fungi were consistently observed and isolated. One was identified as Alanphillipsia ( Ala. ) aloes , and the other three were new to science and are described here as Cytospora euphorbiicola sp. nov ., Nothomicrosphaeropsis namakwaensis sp. nov . and Austrophoma ( Aus .) euphorbiae gen. et sp. nov. These new species and Ala. aloes were the most commonly encountered, and their pathogenicity was tested on E. mauritanica plants in a greenhouse trial. All four species gave rise to lesions that were significantly larger than those associated with the controls, but they were not significantly different to each other. Although the lesions associated with the inoculations were well-developed, they did not give rise to plant death, suggesting that they are not responsible for the large-scale die-off of E. mauritanica in the field. The primary cause of the death of E. mauritanica in the studied area remains unknown and could be due to environmental factors such as has been found with the die-off of Euphorbia ingens in South Africa.

Acacia mangium plantations in Sabah, Malaysia are seriously affected by a vascular wilt and canker disease caused by a species of Ceratocystis. A similar and devastating disease occurs in Indonesia and is caused by the fungal pathogen Ceratocystis manginecans. A closely related fungus, Ceratocystis fimbriata sensu stricto, is a common soil-borne pathogen of sweet potato (Ipomoea batatas) in areas of Malaysia where A. mangium is grown. This study characterised the species causing wilting on A. mangium and compared it with the I. batatas pathogen using DNA sequence-based comparisons used artificial inoculations to assess the effect of the A. mangium pathogen on Acacia auriculiformis and Acacia crassicarpa and considered the ability of the sweet potato pathogen to cause disease on the three Acacia species. DNA sequence comparisons confirmed that isolates from diseased A. mangium were C. manginecans and those on sweet potato were C. fimbriata s.s. Ceratocystis manginecans was pathogenic on all Acacia spp., with A. mangium being most susceptible followed by =A. auriculiformis and A. crassicarpa. Pathogenicity tests showed that C. fimbriata s.s. from sweet potato is not able to cause disease on any of the three Acacia spp. considered. This study also confirmed that C. manginecans is the primary cause of ceratocystis canker and wilt disease in Sabah and that the sweet potato fungus, C. fimbriata s.s., poses no threat to propagated Acacia spp.

Nonnative insects and pathogens pose major threats to forest ecosystems worldwide, greatly diminishing the ecosystem services trees provide. Given the high global diversity of arthropod and microbial species, their often unknown biological features or even identities, and their ease of accidental transport, there is an urgent need to better forecast the most likely species to cause damage. Several risk assessment approaches have been proposed or implemented to guide preventative measures. However, the underlying assumptions of each approach have rarely been explicitly identified or critically evaluated. We propose that evaluating the implicit assumptions, optimal usages, and advantages and limitations of each approach could help improve their combined utility. We consider four general categories: using prior pest status in native and previously invaded regions; evaluating statistical patterns of traits and gene sequences associated with a high impact; sentinel and other plantings to expose trees to insects and pathogens in native, nonnative, or experimental settings; and laboratory assays using detached plant parts or seedlings under controlled conditions. We evaluate how and under what conditions the assumptions of each approach are best met and propose methods for integrating multiple approaches to improve our forecasting ability and prevent losses from invasive pests.

Species of Corymbia are increasingly being tested for plantation establishment in South Africa. During disease surveys in KwaZulu-Natal plantations in 2020, a serious canker disease was found on Corymbia henryi. The cankers were seemingly caused by a fungus belonging to the family Cryphonectriaceae. The aims of the study were to identify the fungus causing the disease, to test its pathogenicity and to determine the genetic diversity of a population of isolates from infected trees. Phylogenetic analyses using sequence data for the internal transcribed spacer, beta-tubulin 1 and beta-tubulin 2 gene regions showed that the causal agent of the cankers was Chrysoporthe austroafricana. This is the first record of C. austroafricana causing cankers on a Corymbia species. A pathogenicity trial demonstrated that the fungus could infect C. henryi and cause cankers. Fifteen isolates of C. austroafricana were subjected to population genetic analyses using microsatellite markers. Eleven multilocus genotypes (MLGs) were detected. Mating-type distribution was approximately equal (MAT1-1:MAT1-2 = 8:7). The results indicate that a wide diversity of genotypes of C. austroafricana have undergone a host shift to infect C. henryi. This is a similar situation to that observed for Eucalyptus in South Africa and suggests that research efforts will be required to reduce the risk of Cryphonectria canker limiting afforestation using Corymbia species in the future.

Fungi in the Cryphonectriaceae include some of the most serious pathogens of trees globally. Amongst these, species of Chrysoporthe, previously identified as Cryphonectria, are well known and important pathogens of Eucalyptus propagated in plantations for the production of various wood products. This study considered Cryphonectriaceae isolates collected from stem cankers on Eucalyptus and the native tree, Henriettea seemannii (Melastomataceae) in Colombia. Isolates were identified based on analyses of DNA sequence data and morphology. These were resolved as Chrysoporthe cubensis, C. doradensis and a new species described here as Chrysoporthe colombiana. All three fungi were found on H. seemannii, whereas C. doradensis was found on Eucalyptus. A pathogenicity test on Eucalyptus showed that the three Chrysoporthe spp. could cause disease on these trees, with C. doradensis being the most aggressive. This study provides another interesting example of tree pathogens in the Cryphonectriaceae occurring on native Melastomataceae and infecting Eucalyptus propagated in plantations.

Araucaria araucana is an ancient conifer, native to the mountain ranges in Chile and Argentina. These trees host a large number of organisms, mainly insects, strongly or even exclusively associated with them. The recent emergence of a novel canker disease on A. araucana has emphasised the importance of fungi associated with these iconic trees and has resulted in the discovery of various new species. In this study, we considered the identity of an unknown calicioid fungus consistently found on resin on the branches of A. araucana. Preliminary phylogenetic analyses placed isolates in the recently described sub-class Cryptocaliciomycetidae, closest to Cryptocalicium blascoi. However, the morphology of the ascomata and its occurrence in a unique niche suggested that the closest relative could be Resinogalea humboldtensis (Bruceomycetaceae, incertae sedis), a fungus with similar sporing structures found on resin of Araucaria humboldtensis in New Caledonia. There are no living cultures or sequence data available for either R. humboldtensis or its supposed closest relative, Bruceomyces castoris, precluding sequence-based comparisons. Morphological comparisons of the sporing structures on A. araucana confirmed that the ascomatal morphology of our unknown calicioid fungus and R. humboldtensis are almost identical and resemble each other more so than B. castoris or Cr. blascoi. A phylogenetic analysis based on the small subunit (SSU), internal transcribed spacer (ITS) and large subunit (LSU) rDNA regions resolved our strains into two clades with Cr. blascoi as its closest relative. Further analyses applying the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) based on ITS, mini chromosome maintenance protein complex (MCM7), RNA polymerase II second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF) gene regions, confirmed that strains represent two new species. Based on our morphological observations and phylogenetic analyses, we introduce two new Resinogalea species, R. araucana and R. tapulicola, and reclassify the genus in the subclass Cryptocaliciomycetidae.

Eucalyptus nitens is a cold-tolerant eucalypt that is native to Eastern Australia. Pure E. nitens as well as its hybrids, such as Eucalyptus grandis × Eucalyptus nitens , is propagated commercially in various regions of the southern hemisphere, including South Africa. In a plantation environment, E. nitens is susceptible to a variety of native and invasive pathogens, including Phytophthora alticola and P. cinnamomi . Recently, there have been increasing reports of root and collar rot in E. nitens in South Africa. The severity of this disease was substantially lower among interspecific hybrids of E. grandis × E. nitens compared to purebred E. nitens . In South Africa, the susceptibility of commercially propagated provenances of pure E. nitens and varieties of hybrid E. grandis × E. nitens to Phytophthora species is unknown. Therefore, we conducted greenhouse trials to evaluate the pathogenicity of P. alticola and P. cinnamomi to two families of pure E. nitens , one self-fertilized and the other outcrossed, as well as a single clonal variety of the most widely planted interspecific hybrid, E. grandis × E. nitens . The outcomes from these trials revealed that both self-fertilized and outcrossed families of E. nitens were highly susceptible to the tested Phytophthora species. The severity of root rot was greatest among plants inoculated with P. cinnamomi. The tested interspecific hybrid was tolerant to both Phytophthora species and developed new lateral and fine roots to offset the effects of root rot.

Diseases increasingly threaten the rapidly expanding eucalypt plantation industry of Indonesia. Of these, leaf blight caused by Calonectria spp. is considered amongst the more important problems, causing losses both in production nurseries and plantations. Using DNA sequence data based on the translation elongation factor 1-alpha, β-tubulin, calmodulin, and histone H3 gene regions, 163 isolates of Calonectria spp. obtained from diseased eucalypt seedlings in nurseries and infected leaves in plantations were identified as Calonectria acicola, C. hawksworthii, C. lombardiana, C. multiseptata, C. pseudoreteaudii and C. reteaudii. Of these, C. lombardiana was by far the most commonly isolated and accounted for approximately 84% of the isolates. Given the predominance of this fungus, it is interesting that it has not previously been reported from Indonesia. This is also the first report of C. pseudoreteaudii and C. acicola from the country. All six species of Calonectria were found to be pathogenic to eucalypts in artificial inoculation studies. Calonectria lombardiana was generally the most pathogenic species and eucalypt genotypes displayed different levels of susceptibility, providing confidence that disease caused by this fungus can be reduced by selecting disease-tolerant planting stock.

Austropuccinia psidii, the causal agent of myrtle rust, has emerged as a significant threat to Myrtaceae in planted and natural woody ecosystems. The first detection of A. puccinia in South Africa was from severely infected ornamental Myrtus communis. This raised concern that M. communis, the sole Myrtaceae species native to Europe and an important component of vegetation in Mediterranean regions, could be threatened by the rust. In light of the potential threat to this unique species, seed was collected from 12 Italian provenances of M. communis, including mainland and island (Sardinia and Sicily) populations. We assessed the susceptibility of these provenances to both the pandemic and South African strains of A. psidii. In Colombia, where the pandemic strain of A. psidii is native, seedlings rapidly became infected by natural inoculum. In South Africa, a preliminary screening of seedlings by artificial inoculation with a single-uredinium isolate produced high levels of disease. Finally, plants of each of the 12 provenances were planted and monitored in Florence, Italy. To date, these showed no signs of disease, but will continue to be monitored. This study highlights the significant threat that both the pandemic and South African strains of A. puccinia pose to M. communis in Europe.

Cankers leading to branch, stem and plant death were observed on the South African endemic Rafnia amplexicaulis ( Fabaceae ) in the Cederberg Wilderness Area, South Africa, during September 2021. Conidiomatal pycnidia were found developing on the cankers, and isolations consistently yielded a Microsphaeropsis species. Phylogenetic analysis based on partial nucleotide sequences of the internal transcribed spacers (ITS), the nuclear large subunit (LSU) and RNA polymerase II second largest subunit ( RPB2 ) regions showed that the fungus represented an undescribed species. Based on the multigene phylogeny and morphological characteristics, we describe the species here as M. rafniae sp. nov . Pathogenicity tests and the fulfilment of Koch's postulates confirmed that M. rafniae sp. nov . is the cause of the cankers of R. amplexicaulis . Presently, this disease is known from a single location in South Africa, and further surveys are required to determine its distribution and relative importance.