Microsatellite markers were used to analyze genetic diversity of four channel catfish (Ictalurus punctatus) populations (Texas,Local,Alabama and Mississippi).The results showed that the allele number of the four populations ranged from 2 to 18,the average effect alleles ranged from 5.820 8 to 6.146 6,the average observed heterozygosity (Ho) ranged from 0.653 0 to 0.693 5,the average expected heterozygosity (He) ranged from 0.732 7 to 0.756 6,and the average polymorphic information content (PIC) ranged from 0.613 5 to 0.725 6.Most loci were significantly deviated from Hardy-Weinberg equilibrium (P <0.05) and the genetic deviation index (D) were almost minus,suggesting loss of Heterozygous in the 4 populations to some extent.Nei’s genetic distance and genetic identity showed that the genetic distance between Texas and Mississippi population was the highest (0.275 0) and the genetic identity was the lowest (0.759 6),while the genetic distance between the population Texas and Local was the lowest (0.139 4) and the genetic identity was highest (0.869 8).The AMOVA result showed that 4.22% of genetic variation was from populations and 85.86% was from individuals.The UPGMA phylogenetic tree of the four populations was constructed based on Nei’s genetic distance.The result showed that Mississippi population clustered into one group,the populations of Texas,Local and Alabama clustered into another group and the relationship between Texas and Local population was the closest.All the results above showed that the four channel catfish populations had high levels of genetic diversity,had the potential as breeding material and then can be used as breeding material.