Abstract: To monitor the fish composition and diversity in the Chongqing section of the Qujiang River, the environmental DNA (eDNA) technology was used, so as to provide references for fish resource monitoring and diversity protection in this river section. Three sampling points, Qingcaoba, Laitan and Mengshutuo, were set up in the Chongqing section of Qujiang River in May 2023. Then collect the water samples and extract DNA. After amplification with 12S rRNA universal primers, sequencing was carried out, and the sequencing results were annotated and analyzed. The results showed that a total of 60 fish species belonging to 6 orders, 10 families, and 47 genera were detected at the three sampling points in the Chongqing section of Qujiang River, including one national protected fish species (Procypris rabaudi), two key protected fish species in Chongqing, eight endemic fish species in the upper reaches of the Yangtze River, and four alien fish species.The relative sequence abundance of Xenocypris davidi was the highest in Qingcaoba sampling point and Laitan sampling point, and the relative sequence abundance of Culter dabryi was the highest in Mengshutuo sampling point. Among the Alpha diversity indices at each sampling point, The Chao1 index was the highest in Laitan sampling point. Moreover, the Shannon index, Simpson index and Pielou index of the Laitan sampling point were statistically higher than the three indexes of qingcaoba and Mengshutuo sampling point. PCoA analysis based on the Bray-Curtis distance matrix in Beta diversity analysis showed that each sampling site showed statistically significant differences in fish community composition. The above results suggest that eDNA technology exhibits high timeliness and reliability when analyzing the composition and distribution of fish diversity in the Chongqing section of the Qujiang River. It has significant application potential in fish resource monitoring and can serve as an important supplement to traditional monitoring methods.