Monitoring and quantifying biodiversity in water bodies using environmental DNA is one of the key technological advances in aquatic ecology in recent years.Environmental DNA technology not only provides rapid and accurate community identification results and species diversity information，but also can be used for relative abundance assessment of species.Zooplankton play a role in energy and material transfer in the aquatic food chain，and can quickly and timely reflect the ecological environment.Based on the eDNA and morphological identification methods of zooplankton in Bali lake and Saicheng lake，the species composition，biodiversity，relative abundance，and community structure characteristics of zooplankton were explored and analyzed.The results showed that the eDNA identification method identified more taxa than morphological identification，with the advantage of higher identification depth，but also had the risk of false positives；there were some significant differences in the results of the two methods in terms of biodiversity representation.