D. maculates is a kind of specialized Schizothoracinae fish has been locally listed as a protected animal in Xinjiang Province,China. Ili River located in north of Tianshan Mountain and Tarim River located in north of Qinghai-Tibetan Plateau were two main distribution areas of this fish. To investigate the genetic diversity and genetic structure of D. maculates,four populations from Tarim River system and two populations from Ili River system were collected in this study. A 570-bp sequence of the control region was obtained for 105 specimens. Twenty-four haplotypes were detected from six populations,only Kunes River population and Kashi River population shared haplotypes with each other. For all the populations examined,the haplotype diversity(h) was 0.904 8±0.012 6,nucleotide diversity(π) was 0.027 9±0.013 9,and the average number of pairwise nucleotide differences(k) was 15.878 3±7.139 1. The analysis of molecular variance(AMOVA) showed that 86.31% of the total genetic variation was apportioned among populations,and the variation within sampled populations was 13.69%. Genetic differences among sampled populations were highly significant. F st statistical test indicated that all populations were significantly divergent from each other(P <0.01). The largest F st value was between Yurungkash River population and Muzat River population,while the smallest F st value was between Kunes River population and Kashi River population. NJ phylogenetic tree of D-loop haplotypes revealed two main clades. The neutrality test and mismatch distribution analysis suggested that the fish had went through a recent population expansion. The uplift of Tianshan Mountain and movement of Qinghai-Tibetan Plateau might contribute to the wide genetic divergence of D. maculates in northwest China. D. maculates is a kind of specialized Schizothoracinae fish has been listed listed as a protected animal in Xinjiang Province, China. Ili River located in north of Tianshan Mountain and Tarim River located in north of Qinghai-Tibetan Plateau were two main distribution areas of this To investigate the genetic diversity and genetic structure of D. maculates, four populations from Tarim River system and two populations from Ili River system were collected in this study. A 570-bp sequence of the control region was obtained for 105 specimens. Twenty For all the populations examined, the haplotype diversity (h) was 0.904 8 ± 0.012 6, nucleotide diversity (π) was 0.027 9 ± 0.013 9, and the average number of pairwise nucleotide differences (k) was 15.878 3 ± 7.139 1. The analysis of molecular variance (AMOVA) showed that 86.31% of the total genetic variation was apportioned among populations, and the variation within sampled populations was 13.69%. Fast statistical test indicated that all populations were significantly divergent from each other (P <0.01). The largest F st value was was between Yurungkash River population and Muzat River population, while the smallest F st value was between Kunes River population and Kashi River population. NJ phylogenetic tree of D-loop haplotypes revealed two main clades. The neutrality test and mismatch distribution analysis suggested that the fish had went through a recent population expansion. The uplift of Tianshan Mountain and movement of Qinghai-Tibetan Plateau might contribute to the wide genetic divergence of D. maculates in northwest China.