Genetic diversity of grass carp was studied by using microsatellite DNA markers, on the wild population from Jiangsu Hanjiang National Four Major Chinese Carps Seed Farm and the cultured populations from Freshwater Fisheries Research Center Aquatic Breeding Farm and Wuxi Qianzhou Aquatic Breeding Farm. The number of alleles generated from each locus ranged from two to eight at the ten assessed loci. The number of effective alleles (ae), polymorphic information content (PIC), expected heterozygosity (He) and the average observed heterozygosity (Ho) were all the highest in Hanjiang wild population as 3.9, 0.506 8, 0.693 9, 0.7 respectively. Meanwhile Wuxi Qianzhou cultured stock had the lowest value: 2.2, 0.179 6, 0.523 5, 0.528 6 respectively. All these parameters of FFRC population were between the above mentioned data, being: 3.5, 0.290 2, 0.541 8, 0.542 9 respectively. All those results showed that the genetic diversity of wild population was more sufficient than that in the cultured populations. Coefficients of gene differentiation (Gst) between Hanjiang wild population and FFRC population, as well as Qianzhou population being 0.219 and 0.246, which were larger than those between the two cultured populations being 0.034. This indicated that the gene differentiated more seriously between wild and cultured populations than those between cultured ones. χ2 significance test for the relative magnitude of genetic differentiation (FST) showed that three loci GM18, MFW1-1, MFW1-2, differentiated most significant among populations; GM03-2,MFW5 significant, others insignificant. HardyWeinberg equilibrium was detected for each population over per loci. The results showed that GM03-1, GM03-2, GM18 deviated from the equilibrium in cultured population for heterozyosis deficiency and GM19 in wild ones for heterozyosis excess. According to our study, inbreeding may decrease the genetic diversity and accelerate homozygotes of the offspring.