Ark shell Scapharca broughtonii is one of the most commercially important bivalve resources and is widely distributed in northeastern Asia. The aim of this study was to determine its genetic structure in Japan, China, and Korea by means of nucleotide sequence analysis of a 507-bp portion of themitochondrial DNA cytochrome c oxidase subunit I gene. Of 180 individuals collected from three localities in Japan and one locality each from China and Korea, a total of 66 haplotypes were found on the basis of 56 variable nucleotides. Although Japan and Korea populations shared six common haplotypes, there was no common haplotype between Japan/Korea and China. The pairwise F_ST and genetic distance values were comprehensively high, with significant differences between Japan/Korea and China, indicating that the divergence had reached subspecies level. In conclusion, haphazard transplantation and import of seedlings and/or adults of S. broughtonii and its related species should be absolutely avoided as S. broughtonii had previously shown distinct genetic differences between Japan/Korea and China.