The microsatellite primers of 8 pairs were used to study genetic variation of the grass carp (Ctenopharyngodon idella) in three progeny groups: YZ (Yangtze River ♀× Zhujiang River ♂),YY (Yangtze River ♀× Yangtze River ♂) and ZZ (Zhujiang River ♀× Zhujiang River ♂) from the populations of Yangtze River and Zhujiang River. The result suggested the number of alleles generated from each locus ranged from two to six at the eight assessed loci which showed rich polymorphism. These microsatellite primers could be used as good molecular markers for the genetic variation study of the grass carps. The number of effective alleles (N_e),observed heterozygosity (H_o),expected heterozygosity (H_e) and polymorphic information content were all the highest in YZ group as 2.811 1,0.984 3,0.639 9,0.559 8 respectively. Meanwhile,ZZ group had the lowest values: 2.675 1,0.865 0,0.612 9 and 0.528 3 respectively. The UPGMA and NJ trees based on genetic distance demonstrated that YZ group was genetically near to YY group. F_st and AMOVA analysis of all groups and loci indicated that there was moderate divergence between YY group and ZZ group. The highest genetic diversity that existed in YZ indicated this hybrid had the high potential for further breeding. There was obvious divergence between Yangtze River and Zhujiang River populations of grass carp.