The catfish, Silurus asotus, is an important commercial fish in East Asia, and it is widely distributed throughout rivers and freshwater lakes of China.Unfortunately, population quantities of S.asotus decreased sharply in recent years because of overfishing and habitat fragmentation. Genetic diversity and population genetic structure are important aspects of the population genetics of fish, and provide essential information for understanding local adaptation and dispersal patterns, and for clarifying the genetic variation. Cytochrome b (Cytb) has a moderate evolutionary rate and a clear evolutionary pattern, suitable for the studies of phylogenetic evolution at the intra- and inter-specific levels. To identify the genetic diversity and population history among geographic populations of S.asotus in different water systems in China, including Yangtze River, Pearl River, Liao River and Southeast coastal rivers, and clarify its population demographic history and genetic structure, the genetic diversity, structure, differentiation, and molecular variance were analyzed using DNAsp5.10.01 and Arlequin 3.11. In the present study, 1110 bases of mtDNA Cytb gene were obtained from 216 of S. asotus collected in the different water systems in China from 2011 to 2012. Generally, there exists high diversity between haplotype (H_d=0.948±0.009) and nucleotide (P_i=0.017 99±0.000 55) in all populations of the catfish, suggesting that the populations were relatively large and stable. In addition, seventy-eight haplotypes, Hap45 was shared in individuals of all populations. Phylogenetic analysis of the MEGA5 was conducted to determine the relationships between S.asotus haplotypes, and detect discernible groups related to geography, and these analyses distinguished four inclusive clades. Moreover, the median-joining network was similar to the topology of the phylogenetic tree with 78 haplotypes, and revealed obivously four lineages in phylogeographic pattern. The results of neutrality tests on S.asotus data set of the four lineages, combined with the nuimodal mismatch distribution, indicated recent population expansion of S. asotus on large spatial scales in the period of late Pleistocene (0.04-0.05 Ma).