The red alga Asparagopsis taxiformis comprises six cryptic mitochondrial lineages (L1–L6) that are genetically distinct but morphologically cryptic. While these lineages occur across tropical and subtropical oceans worldwide, the phylogeographic structure of Korean populations has remained poorly understood. In this study, 39 individuals were collected from eight coastal localities in Korea and analyzed together with global samples. Phylogenetic analyses of concatenated cox2-3 spacer and partial cox1 sequences revealed that all Korean A. taxiformis samples belong to Lineage-2 (L2), a cosmopolitan lineage distributed across multiple ocean basins. Within Lineage-2, the cox2-3 spacer network displayed a consistent global pattern where the H1 haplotype predominated worldwide, including in Korea, whereas private haplotypes were primarily concentrated in Mediterranean populations, especially in Italy. The cox1 network provided higher resolution, resolving three dominant haplotypes (H1-H3) with distinct geographic ranges in East Asia: H1 mainly in the East Sea and Jeju Island; H2 mainly along the south and west coasts of Korea and Jeju Island; and H3 largely in the Ryukyu Islands. Despite this geographic structure, only one to three mutational steps separate these three haplotypes. Organelle genomic analysis of Korean, Italian, and American individuals further demonstrates that Lineage-2 exhibits low to intermediate divergences, a conserved trait despite its broad global distribution compared to other Rhodymeniophycidae species. Demographic and palaeoceanographic reconstructions suggest that the eastern Italian and southern Korean Peninsula served as refugial areas for Lineage-2, although the mechanisms maintaining this conserved, widespread structure remain unknown.
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