is an endemic fish in Xinjiang but the population is decreasing because of human activities and natural environmental changes. To understand the population genetic diversity and structureof, 143 specimens from seven populations in the Kumalake, Muzat, Taxkorgan, Karakax, Yurunkax, Kezilesu, and Qarqan Rivers were collected, the mitochondrial DNA control region was sequenced, and 39 haplotypes were detected. The Qarqan River population did not share haplotypes with any other population, and the FST tests were highly significant between the Qarqan and other populations. Analysis of molecular variance showed that most of the variation was apportioned among the populations, whereas the variation within populations was 81.01%, except that of the Qarqan population. Gene flow among populations varied from 0.0464 to 18.2786 and was < 1 between the Qarqan and other populations. A phylogenetic tree constructed using the Bayes method was consistent with the haplotype network, and the tree was divided into two clades. The most recent common ancestor of the two branches was 2.7 Ma. A mismatch analysis showed a bimodal distribution, indicating geographic isolation between the two branches generated by aridification and salinization of Lop Nor at 2.7 Ma, and Lop Nor subsequently recovered because of the cold and wet climate of the Tarim Basin. Secondary contact resulted in the present-day distribution pattern. The results of a population structural analysis suggested the presence of two distinct geographic populations, such as the Tarim River and Qarqan River populations. The former had high haplotype diversity (0.939±0.008) and nucleotide diversity (0.0125±0.0017), whereas the latter had higher haplotype diversity (0.903±0.025) and lower nucleotide diversity (0.0051±0.0012). These results suggest that different management strategies should be adopted for these two groups, and that the Tarim River population should be protected as a priority.