The mtDNA CO Ⅰ(624 bp), Cyt b (712 bp) and D-loop (457 bp) gene fragments of Aspiorhynchus laticeps and Schizothorax biddulphi were sequenced by PCR respectively and sequence comparisons were made to identify differentiation. The percentage of A+T content was higher than that of G+C content in three gene fragments. There was a strong bias against G content, especially in the third codon positions of protein-coding genes ( CO Ⅰ and Cyt b ). Sequence analysis indicated that the variation of intra-species was low and the nucleotide substitution rate of three gene fragments arranged from high to low was D-loop>Cyt b > CO Ⅰ. The estimated divergence time between two Schizothoracine species based on Cyt b gene was about 3.57 MaBP in Pliocene, which was earlier than the specialized grade and high specialized grade species. Because the Tarim River lies in the northern edge of the Qinghai-Tibet Plateau and is geographical development as a part of the Tibetan Plateau, the uplift of Qinghai-Tibet Plateau influences the evolution of Schizothoracine species in Xinjiang to some extent.