Background: The Xieqiao River Endemic Fish National Aquatic Germplasm Resources Reserve located in Tongren City, Guizhou Province, China, has abundant fish resources. Accurate monitoring of the composition and diversity of fish communities is of vital importance for assessing the health of ecosystems, protecting biodiversity and endangered species, ensuring the sustainable utilization of fishery resources and managing invasive species. 
 
Methods: We examined the distribution and abundance of fishes in water and sediments of the upstream, midstream and downstream of Xieqiao River using eDNA (environmental DNA) metabarcoding. 
 
Result: We recognized 112 fish species belonging to 16 orders, 28 families and 73 genera. The most abundant fishes in Xieqiao River at order, family, genus and species level were Cypriniformes, Xenocyprididae, Opsariichthys and Opsariichthys bidens, which varied in different habitats. Forty-three dominant fish species were identified, including 3 species of specially protected fish in China, 26 endangered species of China Red List of Biodiversity&middot;Freshwater fish, 17 species with extremely high relative sequence abundance in Guizhou Province and 7 species of endemic fish of the upper Yangtze River and 14 alien species. The Chao1 index of water samples are higher than that of sediments (P&lt;0.05). In addition, the fish communities of water in river were different from those in reservoir. In conclusion, the Xieqiao river is rich in fish resources and diversity, but the invasion of alien species should be vigilant. This study assessed fish resources and provides reference for subsequent management of Xieqiao river endemic fish national aquatic germplasm resources reserve.

Fish Diversity in Xieqiao River Endemic Fish National Aquatic Germplasm Resources Reserve based on eDNA Metabarcoding