Catfish, important economic fishes, account for about one-third of the freshwater fishes globally, and are widely distributed with abundant species and population structures in China. Owing to limited bones in the muscle and good taste, catfishes are widely consumed and occupy an important position in the aquatic products market. In this study, using the COI (cytochrome oxidase subunit I) gene fragment as a molecular marker, phylogenetic analyses were carried out on some catfish species. A total of 134 sequences of 13 species of catfishes were amplified using universal primers, and the results were compared with 51 other sequences belonging to 15 species of catfishes obtained from GenBank. The results showed that Pelteobagrus fulvidraco included five insert-deletion sites. The average base A+T (55.5%) was significantly higher than that of G+C (44.5%). The average genetic distance of 28 pairwise and 23 within species were determined as 0.195 and 0.006, respectively using Kimura's 2-parameter (MEGA6.0). The phylogenetic tree analysis showed that a neighbor-joining tree was more suitable than the maximum likelihood tree for the genetic analysis of the catfish species. According to neighbor-joining tree for all 185 sequences of catfishes, the consistency with traditional taxonomy on family levels and below was higher (82.9%) than that of order levels (71%). Samples of each species formed highly supported monophyletic groups. The neighbor-joining tree showed that species of come from the same branch, and the . The results of this study showed that the COI gene could be used as a molecular assistive tool for the identification of catfish species, and could also be applied to molecular phylogenetic relationships. The results effectively expanded the species classification information of catfishes, and provided necessary evidence for traditional taxonomy.