Schizopygopsis kialingensis is an endemic fish of the Bailong River, which is a tributary of the Jialing River. The species' population has been largely reduced in recent years as a result of overfishing, river pollution, and dam construction. To develop effective strategies forpreserving the species'germplasm, it is first necessary to understand the species' genetic variation and population structure. Therefore, in the present study, a 706-bp segment of the mitochondrial control region was sequenced from 147 S. kialingensis specimens that were collected from six populations in the Bailong and Weihe Rivers. Seventeen variable sites and 14 haplotypes were identified. The six populations exhibited high haplotype diversity (0.810) and low nucleotide diversity (0.00698), and the genetic diversity of the Zhouqu County Chengguan Township population was highest, whereas that of the Weiyuan County Qiaoyu Township population was the lowest. AMOVA indicated that significant difference among populations, with 44.29% molecular variation among the populations and 55.71% molecular variation within populations. Pairwise fixation index (Fst) values indicated that all the populations were significantly different, except the Tanchang County Nanhe Township and Zhouqu County Chengguan Township populations. Meanwhile, gene flow estimates suggested high levels of gene flow, and the Mantel test indicated that the genetic and geographic distances were significantly correlated. In addition, the construction of a neighbor-joining phylogenetic tree and a minimum spanning network indicated that the 14 haplotypes formed two main groups that corresponded to the Bailong River and Weihe River systems, and mismatch distribution and neutrality analyses indicated that the population has not under gone recent expansion. According to these findings, we suggest that the S. kialingensis population in the Bailong River should be protected and that the protection of the Weihe River population should be prioritized, owing to the group's high genetic differentiation and very low genetic diversity.