In the present study,294 Schizothoracinae specimens of Schizopygopsis pylzovi, Gymnocypris chilianensis and Schizopygopsis kialingensis,were collected from 8 sampling sites from the Yangtze River,the Yellow River and inland rivers in Gansu Province.Mitochondrial DNA Cyt b gene was used as molecular marker to perform the phylogenetic analyses,genetic diversity and population differentiation analysis of the 3 Schizothoracinae fishes.Phylogenetic analyses of all haplotypes based on NJ and BI methods revealed that S. pylzovi was clustered as a monophyletic group.However, S. kialingensis was clustered into a clad with G. chilianensis,suggesting that the two species are under early stage of speciation.Genetic diversity analysis showed that a total of 23 haplotypes were detected in the Cyt b gene of 70 S. pylzovi,with the haplotype diversity and nucleotide diversity being 0.917 and 0.003 10,respectively.A total of 28 haplotypes were detected in the Cyt b gene of 132 G. chilianensis,with the haplotype diversity and nucleotide diversity being 0.819 and 0.009 82,respectively.A total of 13 haplotypes were detected in the Cyt b gene of 92 S. kialingensis,with the haplotype diversity and nucleotide diversity being 0.706 and 0.002 33,respectively.No haplotypes were shared between either two different species,and significant population differentiation were detected among geographic populations,showing that geographic isolation has a significant impact on these Schizothoracinae fishes,and adaptive differentiation as well.Hence,different populations should be treated as different evolutionary significant units in conservation management.