Macrobrachium nipponense in Hongze LakeBFG），，observed heterozygosity and expected heterozygosity under Hardy-Weinberg equilibrium were estimated to characterize genetic diversity. Tests to detect excess heterozygosity in a population at mutation-drift equilibrium were analyzed. The results showed that all the 8 loci were highly polymorphic.Tests of departures from Hardy-Weinberg equilibrium indicated at least 5 loci in each stock were with significant heterozygosity deficiency. There was significant deviation from Hardy-Weinberg Equilibrium in all stocks. All of the 9 stocks in Hongze Lake showed high genetic diversitiesand the genetic diversities of stocks in eastern and central Hongze Lake such as BFJ and JB were higher than those in the western lake including BJ and JJ. The oriental river prawn stocks in Hongze Lake were partly different from mutation-drift equilibrium with partly heterozygote excessesF_ST and AMOVA analysis across all stocks and loci indicated that there was medium level of divergence among the 9 stocks. NJ and UPGMA clustering tree based on genetic distance demonstrated that the stocks of adjacent geographical position clustered together.