Marsupenaneus japonicusis one of the important species in shrimp fisheries and aquaculture in China.Two morphologically similar varieties(Ⅰ and Ⅱ)with distinct color banding patterns on the carapace are recognized from the South China Sea.In the present study,9 pairs of microsatellite markers were used to detect the genetic diversities from two varieties of 6 wild stocks of M.japonicus,i.e.Zhoushan(ZS)stock in Zhejiang province,Xiamen(XM)stock in Fujian province,Huilai(HLQ and HLB)stock in Guangdong province,Lingshui(LS)stock in Hainan province and Beihai(BH)stock in Guangxi province.The results indicated:a total of 235 alleles were obtained from 9 markers in the 6 stocks.Polymorphic information content(PIC)value per locus was more than 0.5,indicating the 9 loci seemed highly polymorphic.Basic data statistics showed that the mean observed alleles in each stock were 13.2-17.7.The mean observed heterozygosity(H_o)ranged from 0.729 6 to 0.788 9 and the mean expected heterozygosity(H_e)ranged from 0.880 5 to 0.925 1.Average polymorphism information content(PIC)was 0.851 2-0.903 5,which explained high level of genetic diversity in 6 wild stocks.42.6% of stock loci showed significant deviation from the Hardy-Weinbery balance,and there was heterozygosity deficiency in all stocks.The pairwise genetic differentiation(F_st)in 6 M.japonicus stocks ranged from 0.011 8 to 0.091 1,indicating significant genetic differentiation among the 6 stocks.Analysis of molecular variance(AMOVA)revealed that the variation within stocks was 93.06%,whereas the variation among stocks accounted for 6.94% of the total variation.The genetic distance among stocks ranged from 0.178 5 to 0.621 8.Cluster analysis based on D_A indicated that HLB,BH and LS stocks were clustered as one group while ZS,XM and HLQ were gathered in another group.