Abstract: Genetic diversity and genetic structure of 7 wild stocks of oriental river prawn Macrobrachium nipponense in Qiantang River, i.e. Wen-yan, Fu-yang, Chang-kou, Tong-lu, Xin-an-jiang, She-xian and Xiu-ning, were investigated using 10 microsatellite DNA markers. The result showed that all the 10 loci were highly polymorphic. There was a trend that the level of genetic diversity of wild stocks in downstream and midstream were higher than the upstream ones’. Sign test and Wilcoxon sign rank test results showed that the stocks in Qiantang River had no bottleneck effect, and the number of stocks had not declined recently. FST among stocks ranged from 0.0201 to 0.1069. Analysis of molecular variance (AMOVA) revealed that a higher portion (93.48%) of variations existed within individuals, while lower portion (6.52%) existed among stocks. FST and AMOVA analysis across all stocks and loci indicated the medium level of divergence among the stocks. The NJ clustering tree based on DA genetic distance demonstrated that the stocks of adjacent geographical position clustered together. 413 individuals obtained from six wild stocks could be divided into two potential populations based on the genetic structure. This study demonstrated that genetic diversity and genetic structure of M. nipponense stocks were relevant to geographical position where they survived.