The gene sequences of cytochrome oxidase subunitⅠ, cytochrome oxidase subunit Ⅱ and cytochrome oxidase subunit Ⅲ of 12 individuals of Bagarius yarrellis were obtained by PCR technique and clone methods; MEGA5.0 program was used to analyze their phylogeny and polymorphism. It can be seen from the results that the total length of COⅠ gene sequence was 1 551 bp, as well as 12 individuals showed 9 haplotypes and 13 mutation sites; the total length of CO Ⅱgene sequence was 691 bp, as well as 12 individuals denoted 5 haplotypes and 5 mutation sites; the total length of CO Ⅲ gene sequence was 784 bp, as well as 12 individuals showed 7 haplotypes and 8 mutation sites. Phylogenetic analysis reveals that B. yarrelli has a certain sequence homology with 14 species of Sisoridae. The structured Minimum Evolution (ME) phylogenetic tree from sequences of COⅠ, COⅡ and CO Ⅲ showed that B. yarrelli exists in the same branch with Glyptothorax sinense, Glyptothorax fukiensis, Glyptothorax trilineatus and Gagata dolichonema, which indicates that B. yarrelli has a close genetic relationship with species of Glyptothorax and Gagata.