Marsupenaneus japonicus is 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 (Ho) ranged from 0. 729 6 to 0. 788 9 and the mean expected heterozygosity (He) 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( Fst)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 DA indicated that HLB ,BH and LS stocks were clustered as one group while ZS ,XM and HLQ were gathered in another group.%选用9个多态性微卫星分子标记,分析我国近海浙江舟山(ZS)、福建厦门(XM)、广东惠来(HLQ及HLB)、海南陵水(LS)及广西北海(BH)日本囊对虾6个群体2种形态变异类型群体间的遗传变异,探讨了日本囊对虾的种质资源状况.结果显示,9个位点在6个日本囊对虾群体中均为高度多态(PIC ＞0.5),共检测出235个等位基因；6个群体平均等位基因数在13.2～17.7；PIC平均值在0.851 2～0.903 5；平均观测杂合度(Ho)在0.729 6～0.788 9,平均期望杂合度(He)在0.880 5～0.925 1；表明群体遗传多样性水平较高.Hardy-Weinberg平衡检测显示,6个群体普遍存在杂合子缺失现象.分子变异方差分析( AMOVA)结果表明,遗传变异6.94％来自群体间,93.06％来自群体内.由ZS、XM和HLQ群体组成的形态变异类型I与由HLB、LS和BH群体组成的形态变异类型Ⅱ之间的Fst均大于0.05,发生了中等程度的遗传分化；相同形态变异类型各群体间的Fst均小于0.05,遗传分化不明显.日本囊对虾群体间的遗传距离(DA)为0.178 5～0.621 8;UPGMA聚类分析表明,聚类关系符合距离隔离模式,BH群体和LS群体遗传距离最小,亲缘关系最近,它们首先聚在一起,然后与HLB群体聚为一支；XM群体和HLQ群体先聚在一起,再与ZS群体聚为另一支.
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