Genetic diversity and genetic differentiation of 18 stocks of Sinonovacula constricta in Yueqing Bay and Sansha Bay, were investigated by using eight microsatellite loci, in order to evaluate the genetic divergence between Yueqing Bay and Sansha Bay, protecting aquatic genetic resources and providing the basic information of genetic breeding in sourceland of Sinonovacula constricta in China. The results of genetic diversity showed that: the average effective allele numbers (N_e) of Yueqing Bay and Sansha Bay ranged from 8.146 to 10.457 and from 7.457 to 9.947; the average expected heterozygosities (H_e) varied from 0.872 to 0.909 and from 0.846 to 0.894; the average genetic diversity index of Nei’s ranged from 0.863 to 0.899 and from 0.836 to 0.886， respectively. Those data indicated higher genetic diversity in all of the 18 stocks in Yueqing Bay and Sansha Bay. Pairwise F_ST values between stocks of Yueqing Bay and Sansha Bay ranged from 0.000 1 to 0.052 3, which indicated that there was some degree of differentiation among 18 stocks based on F_ST. The UPGMA phylogenetic trees based on D_A genetic distance suggested that the 18 stocks were divided into two groups, one of which included the stocks of ZYC，ZNY，ZNT，ZQJ，ZHW，ZHS and ZLP in Yueqing Bay whereas the other one consisted of ZWY and ZWG in Yueqing Bay and FZW，FMT，FSD，FSJ，FBZ，FXT，FCC，FSJ and FXW in Sansha Bay. As a result, we can infer that the stocks of ZWY and ZWG in Zhejiang province may come from Fujian Province, revealing the introduction phenomenon in the culture of Sinonovacula constricta.