The complete sequences of genes encoding cytochrome C oxidase subunitsⅠ , Ⅱ and Ⅲ were cloned in Schizopygopsis pylzovi by RT-PCR method. The sequence analysis showed that the complete sequence of CO Ⅰ was 1 551 bp, which consisted of the open reading frame (ORF) encoding 516 amino acid residues; the CO Ⅱ gene was 691 bp and contained a 690-nucleotide ORF encoding 230 amino acid residues; and the CO Ⅲ gene was 786 bp, which was composed of the ORF encoding 261 amino acid residues. The homologous analysis of sequences showed high similarity both in DNA and corresponding amino acid sequences of CO Ⅰ , CO Ⅱ and CO Ⅲ between S.pylzovi and other 9 species from family Cyprinidae. Although there were sequence differences in subunit genes among different species, the corresponding amino acids tended to be consistent, suggesting functional stability of cytochrome C oxidase in electron transfer of mitochondrial respiration chain. S.pylzovi and Sinocyclocheilus grahami clustered together in the phylogenetic trees based on gene and amino acid sequences of CO Ⅰ, and gene sequences of CO Ⅱ and CO Ⅲ, coupled with the same types, positions and numbers of functional sites in CO Ⅰ and CO Ⅱ, suggesting that there is a relatively close relationship between them, which is consistent with the conclusion that the subfamily Schizothoracinae is originated from one of the primitive Barbinae fishes widely distributed in warm drainages in Qinghai-Tibetan Plateau during the Tertiary Period.