Ark shell Scapharca kagoshimensis is one of the commercially important bivalve resources in East Asia. In Japan, the mass production method for its natural seedlings was developed in the 1880s, and they had been transplanted to an array of the major fishing areas. It has been therefore concerned with its genetic disturbance among not only current but also former fishing areas in Japan. This study was undertaken to ascertain its genetic diversity and population structure in East Asia by means of nucleotide sequence analysis of a 555-bp portion of the mitochondrial DNA COI gene. Of 225 individuals collected from 8 populations and 1 population in Japan and Korea, respectively, a total of 59 haplotypes, including 14 common haplotypes, were found, and Japan and Korea shared 3 common haplotypes. In Japan, the haplotype diversity and nucleotide diversity ranged from 0.65 to 0.93 and from 0.22% to 0.59%, respectively, reflecting relatively high levels of genetic diversity. The values in Korea were determined to be 0.45% and 0.19%, respectively, indicating significantly lower genetic diversity compared with that in Japan. Mismatch distribution analysis and neutrality tests showed a recent history of multiple types of reproduction and signals of demographic change in each population. These results suggest that S. kagoshimensis has experienced rapid population growth or reduction in population size such as a bottleneck in a short period.