Abstract: Random Amplified Polymorphic DNA (RAPD) was applied to investigate the genetic diversity of six geographic populations of Macrobrachium nipponense, which were collected from the Weishan Lake(WL), Hongze Lake(HzL), Taihu Lake(TL), Longgan Lake(LL), Honghu Lake (HL) and Pearl River(PR). Under optimal conditions, 18 random primers from OPI, OPM, OPP, OPX, were chosen to analyze their genomic DNA (30 individuals of each population). A total of 201 RAPD fragments ranged 100bp~2000bp were obtained, 141 of which were polymorphic (70.15%). For different populations, the proportions of polymorphic loci were 21.13%～55.93%, mean expected heterozygosity varied from 0.1132 to 0.2071, and the Shannon index (I) varied from 0.1695 to 0.2950. Index of genetic diversity Gst ranged from 0.2116to 0.4442 for different populations, and index of genetic diversity Gst0 was 0.4461. Nm ranged from 0.6257 to 1.8628. Results indicated that notable genetic divergence emerged between populations. Clustering of the stocks was analyzed by UPGMA, the results showed that Hongze Lake and Weishan Lake populations, Honghu Lake and Longgan Lake population clustered first respectively, then they clustered with Taihu Lake population, the last did Pearl River population.