Tarim River is the largest one of the inland rivers in China. The genus Schizothorax Heckel has the most abundant and diverse fish in the subfamily of Schizothoracinae distributed in the Tarim River Basin and has a great ecological value of researches. In this study, the phylogenetic relationships of 6 species of fish in genus Schizothorax Heckel collected from Tarim River basin and Yili River basin were analyzed using the mitochondrial COI gene sequences. A total of 25 haplotypes were detected from 419 individuals of samples. The genetic distances among Gunther population of S. biclolulphi collected from the Tarim River main tributary, S. eurystomus (Kessler), S. barbatus McClelland, and S. irregularis Day were all less than 0.005, and no significant "barcode gap" was formed. However, the genetic distances between the Qarqan River population of S. biclolulphi Gunther and other species were accorded with the 2% threshold or the principle of ten times. Both of the ABGD and Taxon DNA analysis identically showed that the Xinjiang Schizothorax Heckel were divided into four groups. Gunther population of S. biclolulphi from Tarim River main tributary, S. eurystomus, S. barbatus and S. irregularis were formed one group. S. pseudaksaiensis, S. argentatus, and S. biclolulphi population from Qarqan River were formed the other three groups, respectively. In the BI phylogenetic tree, the S. biclolulphi Qarqan River population formed an independent branch with a node support rate with 100%. However, S. biclolulphi population from Tarim River main tributary, S. eurystomus, S. barbatus, and S. irregularis failed to form independent branches. The topology of BI tree is consistent with the grouping results of ABGD and Taxon DNA. Interspecific hybridization may be exists among S. biclolulphi population from Tarim River main tributary, S. eurystomus, S. barbatus, and S.irregularis, or these species has not yet reach the interspecific differentiation degree. S. biclolulphi population from Tarim River may have diverged into separate species. These results will provide a reference for analyze the genetic relationship of fish in genus Schizothorax Heckel from Tarim River Basin.