The introduced Japanese scallop has been farmed in China, primarily along the coasts of the Bohai Sea and the North Yellow Sea, since the 1980s. Following the adaptation and localization of in China, specific problems have appeared after several decades of aquafarming: especially low survival and slower grow. This can be associated with an effectively small population that experiences inbreeding, eventually leading to unknown degrees of decline in its genetic diversity after several generations. Consequently, it is important to carry out genetic diversity research on in its main mariculture area of China. In this study, mitochondrial cytochrome-b (Cyt ) gene-sequencing techniques were used to determine genetic diversity and variations among six stocks of : the bottom-sowing cultured stocks of Changdao, Haiyangdao and Zhangzidao; the natural stocks of Lüshun and Japan; and the artificial selected stock of Zhangzihong. A total of 20 haplotypes were found among 120 sequences of Cyt The minimum number of haplotypes was found in the Zhangzihong artificial breeding stock, and the maximum number occurred in the Japan Aomori Mutsu Bay stock, with a haplotype diversity () of 0.10000 and 0.88400, respectively. Analysis of molecular variance (AMOVA) showed the percentage of variation between the Japan and China groups was 15.34%, which was significantly higher than when measured as one genetic pool. For the China group, 83.41% of the genetic variation come from within the stocks, and only 1.52% of the variation was among the stocks in the group, indicating that genetic variation between individuals of the China group was higher than between the stocks. analysis showed a moderate level of genetic variance among the Japan stock and China stocks (0.07455-0.17895, P. yessoensis was calculated based on the Tamura-Nei model; the maximum genetic distance was found between the Japan Aomori Mutsu Bay stock and the Haiyangdao bottom-sowing cultured stock; the minimum genetic distance was found between the Zhangzidao bottom-sowing cultured stock and the Zhangzihong artificial breeding stock. The UPGMA method was used to construct a phylogenetic tree based on genetic distances among the six stocks of ; the tree shows that the five China stocks clustered into a genetic branch, and then these clustered together with the Japan group. These results demonstrate obvious genetic differentiation between the China stocks and the Japan stock of this scallop. Moreover, genetic diversity was lower in the China stocks as compared with the Japanese stock. The findings of this study could be usefully applied to scientific strategies for the protection, sustainable development and commercial utilization of scallop germplasm resources.