are economically important in China, though wild populations have been in serious decline throughout the region. We used microsatellite markers to evaluate the genetic diversity amongst grass carp from four populations in three watersheds (Yangtze River, Pearl River, and Heilongjiang River). We selected 26 microsatellite markers and calculated heterozygosity, polymorphism information content (PIC), valid allele number, allele frequency, genetic distance, genetic similarity coefficient, and Hardy-Weinberg balance deflection index. There was a high degree of polymorphism within the markers in all three watersheds. The mean polymorphism information content (PIC) ranged from 0.581 3 to 0.638 6. Each microsatellite locus had 11 alleles (mean: 5.46). We identified a total of 154 alleles from all four populations, with a mean number of valid alleles of 3.455 6. The heterozygosity was between 0.711 4 and AMOVA analysis across all populations and loci suggested that there was low level of divergence amongst the four populations (=0.031 73). The Jianli population and the Hanjiang population were grouped in one cluster, which was clustered with the Pearl River population. The Heilongjiang population was grouped in a separated cluster. Our results suggest that there is a high level of genetic diversity among grass carp from the three watersheds, and no obvious differentiation. Our results may be used to better manage the fishery for conservation of locally adapted populations.