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Litopenaeus vannamei which is also known as Penaeus vannamei was introduced into China in1987. Litopenaeus vannamei had been achieved in large-scale farming in China after it had been tackled in the intensive breeding and artificial breeding technology. But in recent years, the outbreak of various diseases of shrimp which made the shrimp industry suffer a severe strike and heavy losses. It had a relationship with the germplasm degradation. In view of this, more sophisticated multivariate analysis and microsatellite molecular markers were adopted to study the morphological diversity and molecular genetic diversity of Litopenaeus vannamei from different regions in China. And it should provide a theoretical basis for breeding of fine species of Litopenaeus vannamei.The morphological variation of six populations of Litopenaeus vannamei were investigated by three multivariate analysis techniques in this study. The results of cluster analysis indicated that morphological traits were similar between the Guangdong and Xiamen stocks, but quite different from that of the Zhejiang, Sanya and Hainan stocks (culture water salinity were70%o and10%o). Through principal component analysis, three principal components were established, with their contributory ratio being28.96%,18.22%,14.89%and10.51%, respectively, and the cumulative contributory ratio being72.58%. Discriminant analysis revealed the discrimination accuracy being76.7%-96.6%for P1and82.3%～100%for P2, the integrative discrimination accuracy being88.3%。There were some morphological differences among the six populations, which focused on the carapace characters, but the morphological variation of the six populations was characterized under-subspecies.Genetic diversity of5stocks of Litopenaeus vanname was assessed by5microsatellite markers. The results showed that the numbers of allele of every locus was ranged from3to5. Five sites mean polymorphism information content (PIC) ranged from0.625to0.915in5stocks, was greater than0.500, genetic diversity of the stocks was at a high level. The mean PIC of Xiamen stock was0.75, which was highest. The mean PIC of Guangdong and Zhejiang was0.73, which is lowest. The mean expected heterozygosity (He) was0.56,0.46,0.48,0.59,0.47respectively, and the mean observed heterozygosity(Ho) was0.45,0.51,0.45,0.53,0.37respectively in5stocks. Out of25population-locus cases,17were not accorded with the Hardy-Weinberg equilibrium(D<0). Except the expected heterozygosity (He) of Xiamen stock was greater than observed heterozygosity (Ho), others were inversely related. And we found that the genetic correlation between Hainan (HN2) and Zhejiang was the highest, between Zhejiang and Guangdong the lowest.
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