CONCLUSIONS
Aquatic biodiversity surveys are increasingly adopting fast and nondestructive eDNA methods. This study aimed to demonstrate the diversity and endemicity of fish in the Chishui River by identifying 77 fish species at 52 sites. Fish assemblages in the river displayed significant variation along its longitudinal gradient, with notable differences between the upstream and downstream areas. The driving factors behind this phenomenon were analyzed, indicating that the flow rate and altitude were the most significant environmental factors. In contrast, human factors did not significantly influence the distribution of fish species. Overall, this study highlights the feasibility of using eDNA methods to investigate the Chishui River Basin and provides valuable reference data for the management and protection of fish resources in the upper reaches of the Yangtze River.