In this study, five tailed mussels were collected from the western coastal area of South Korea, and their DNA analyses were assessed by sequencing the partial mitochondrial cytochrome c oxidase subunit I (COI) gene. All DNA sequences were identified as Lingula anatina. These are the first COI record of the L. anatina from South Korea. Furthermore, the COI gene sequences of L. anatina reported from China, Japan, and Hong Kong were retrieved from GenBank, and phylogenetic relationships and genetic distances of the organisms were analyzed. Phylogenetic analysis and genetic distances suggest that the most related population with L. anatina of the present study is the Chinese population. The Japanese population diverged early from a linkage that includes Korean and Chinese populations. The Hong Kong population and one Japanese specimen examined were the most distantly related to other populations. This study provides additional data for phylogenetic study of L. anatina.