Abstract: In order to monitor the status of planktonic algae in Chai River efficiently and quickly, the diversity of planktonic algae in Chai Reservoir and its upstream and downstream sites was studied by using environmental DNA(eDNA)metabarcoding technology and microscopic identification counting method in July 2021. The results showed that the phytoplankton species identified by eDNA metabarcoding technology at the family and genus levels accounted for 72.2%and 37.5% of the microscopic identification counting method respectively. Combined with the two methods, 58 genera, 38families, 30 orders and 9 phyla of phytoplankton were identified in the river; Chlamydomonas was the dominant algae in the upper reaches of the reservoir, Anabaena was the dominant algae in the reservoir, and Rhombus was the dominant algae in the lower reaches of the reservoir; Shannon Wiener diversity index(H') at different sites of Chai River was 1.381 ～ 2.432;Pielou evenness index(J) was 0.398 ～ 0.716; The water quality of different sections of Chai river was evaluated according to the diversity index and evenness index. The upstream of the reservoir was moderately polluted, the reservoir section was moderately polluted, and the main river section at the downstream of the reservoir was lightly polluted. As a new method,e DNA metabarcoding technology can monitor and evaluate the diversity of planktonic algae in Chai River, and provide a basis for ecological health assessment and protection of Chai River.