To understand the distribution of perfect microsatellites in the genome of the channel catfish (Ictalurus punctatus), we used MISA, a bioinformatics software package, to search and analyze the microsatellites. A total of 510 256 perfect microsatellites were isolated from 29 chromosomes of I. punctatus, with a total length of 11 036 941 bp. The chromosome containing the largest number of microsatellites was chromosome 2 (25 284), followed by chromosomes 3, 1, and 5. Chromosome 29 had the lowest number of microsatellites (11 591). The length of each chromosome was significantly correlated with the number of microsatellites it contained (SPSS, r = 0.98, P < 0.01). The highest relative abundance of microsatellites was found on chromosome 27 (785.03 ind./Mb), and the lowest was on chromosome 11 (615.89 ind./Mb). Among the six repeat types, mononucleotides were the most frequent, accounting for 45.31% of the total, followed by dinucleotides (38.53%), trinucleotides (8.73%), tetranucleotides (6.93%), pentanucleotides (0.46%), and hexanucleotides (0.04%). The predominantly repeated microsatellite sequences in the I. punctatus genome were A, AC, AG, AT, AAT, AAAT, C, AAC, AAAC, and AAG, showing an obvious inclination towards A and T bases. The results of this study provide a reference for the further study of I. punctatus genome characteristics and contribute basic data for future investigations into molecular marker-assisted breeding and genetic information assessment of I. punctatus.