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Inferring phylogeographic patterns of macroalgal species is essential for understanding the population structure and for the conservation of macroalgal species. In this study, the phylogeographic patterns of two co-distributed macroalgal species along the coast of Korea and Japan, <i>Pachymeniopsis lanceolata</i> and <i>Pachymeniopsis elliptica</i>, were analyzed. <i>Pachymeniopsis lanceolata</i> (215 specimens from 36 sites) and <i>P. elliptica</i> (138 specimens from 24 sites), using the plastid <i>rbc</i>L gene, are characterized by fifteen and six haplotypes, respectively. Mitochondrial COI-5P gene sequences revealed a low variation for both species. An analysis of molecular variance (AMOVA), pairwise <i>F_ST</i> comparisons, and haplotype networks based on the <i>rbc</i>L data suggest a weak genetic differentiation of both species. The shared haplotypes (<i>P. lanceolata</i>: LR01; <i>P. elliptica</i>: ER01) found in the entire sampling range indicate that these two <i>Pachymeniopsis</i> species can disperse over long distances along the coast of Korea and Japan. Despite the similar phylogeographic pattern, our results suggest that <i>P. lanceolata</i> has a higher genetic diversity, with a wider distribution along the Korean Peninsula than <i>P. elliptica</i>. Moreover, it is adapted to low sea surface temperatures and survived in more of the available habitats during periods of climatic change, whereas <i>P. elliptica</i> is less adaptable and more susceptible to environmental disturbance. This phylogeographic study provides a rationale for the conservation of the wild <i>Pachymeniopsis</i> population.