The mountainous regions of Southwest China are biodiversity hotspots where geographical isolation promotes genetic differentiation and species diversification. For cave-dwelling species like the , how geographical isolation, historical climate, and riverscapes have influenced their evolution remains largely unexplored. Based on 255 samples from the Pearl River and the Yangtze River, this study integrated two mitochondrial genes and two nuclear genes to analyze the genetic diversity and structure of the population. Phylogenetic trees based on mitochondrial DNA revealed two distinct clades of , while nuclear DNA loci showed no clear separation. Spatial Analysis of Molecular Variance (SAMOVA) confirmed two groups: Clade I (the Yangtze, the Guijiang, and the Duliujiang Rivers) and Clade II (the Nanpanjiang, Hongshui, Dahuanjiang, Youjiang, and Rongjiang Rivers). The divergence time between the two clades was estimated at 13.73 million years ago, which was potentially linked to the impact of the QTP uplift on monsoonal systems. The star-like network analysis and neutrality test results indicated that the population of Clade I has maintained a stable state over a long period, while the population of Clade II showed a trend of expansion. Additionally, geographical features such as the Nanling Mountains and the two major river systems may have obstructed gene flow, leading to genetic differentiation. These findings improved our understanding of this species' evolutionary history and population structure, offering valuable insights for conservation efforts.