Abstract：The channel catfish (Ictalurus punctatus) was introduced from America to China in the 1984. It has been cultured on a large scale in 20 provinces of China. EST-SSRs was used to analyze the genetic diversity of domestic stocks of channel catfish (Ictalurus punctatus).The four populations were the population in Fuzhou province and Hubei province which introduced in 1984(P1984), the population in Fuzhou province and Liaoning province which introduced in 1997(P1997), the population in Hunan province which introduced in 2004(P2004),and the population in Fuzhou province which was cross breeding between P1984 and P1997(P8497). EST-SSR marker is a new kind of SSR markers which is developed from the ESTs. It not only act as genetic markers, but also reveal differences in related gene expression. In this study, two gene sites were found whose functions were clear. Thirty individuals from each population were analyzed．Amplifications were performed in a PCR reactor for the genetic diversity with 10 EST-SSRs markers. All the primer sets produced discernible DNA fragments, of which 9 primer showed polymorphism. In this study, 32 alleles were obtained．The number of alleles of each locus ranged from 2 to 4, and allele size ranged from 100 to 212 bp. The mean number of alleles (A) ranged from 3.0000 to 3.4000. The mean number of effective alleles (ae) ranged from 1.9455 to 2.3024. The average observed heterozygosity (Ho) for the four populations was 0.5334, 0.4768, 0.5982, and 0.5092, respectively. The average expected heterozygosity(He) for the four populations was 0.4943, 0.5695, 0.4913 and 0.5091, respectively. PIC (Polymorphism Information Content) per locus ranged from 0.4113 to 0.4829. The difference in genetic diversity among the four populations is not significant, and the genetic diversity of four populations was in moderate level. According to gene differentiation (Gst), genetic distance (D), Genetic similarity (S) and UPGMA, we found that the relationship between P1984 and P8497 was nearest, and the relationship between populations P1984 and P2004 was farthest, which proves the order that introduced into China among the four populations. The P value test of Hardy-Weinberg equilibrium showed that 18.75% loci departed from Hardy-Weinberg equilibrium. The results of the F-statistics suggested the surplus heterozygosity for P2004 and P8497, and the absent heterozygosity for P1984 and P1997, and low genetic differentiations among the four populations，and mainly differentiations due to individual difference.
