Abstract:In order to understand the diversity and community characteristics of the plankton community in the Rare and Endemic Fish National Nature Reserve in the Upper Yangtze River in Chongqing Section, six sampling sections were set up in this river section for sample collection in March 2021. The diversity and community structure characteristics of the plankton community in this section of the river were investigated by combining the environmental DNA technology (eDNA technology) and the traditional morphological identification methods (traditional methods). The results showed that: 1) 118 genera of eukaryotic zooplankton were detected in all the samples, among which 7 phyla and 62 genera of eukaryotic phytoplankton were detected, mainly Chlorophyta and Bacillariophyta algae; and 4 groups and 56 genera of zooplankton were detected, mainly Protozoa. 2) The average density of eukaryotic phytoplankton was 8794 2×104 individuals·L-1 with an average biomass of 0114 98 mg·L-1; while the average density of zooplankton was 0014 33×104 individuals·L-1 with an average biomass is 0896 43 mg·L-1. 3) The average ShannonWiener diversity index of phytoplankton and zooplankton calculated by traditional method were 2869 0 and 2230 8, and the mean values of Pielou evenness index were 0876 2 and 0926 0. The mean values of the above two indices calculated based on the number of eDNA technology sequences were 5229 7 and 4280 5 for phytoplankton in each sampling section, and 0552 7 and 0704 1 for zooplankton. The biodiversity index revealed that the water quality in the Chongqing section of the reserve is currently in a state of βmoderate pollution to light pollution or no pollution. Overall, the results suggested that eDNA technology can be combined with traditional methods to explore the characteristics of plankton diversity and community structure in monitoring and evaluating freshwater plankton resources at this stage.