Phytoplankton and zooplankton are the primary producers and consumers of aquatic ecosystems, respectively. Their accurate identification is the basis for aquatic ecology research. Traditional identification of phytoplankton and zooplankton based on morphological characteristics of species is time-consuming and labor-consuming, difficulty in identification, and underestimating species diversity. Therefore, a simple, efficient, accurate and standardized solution for studying biodiversity of zooplankton and phytoplankton is very necessary. Environmental DNA (eDNA) metabarcoding technique has become a common method for studying aquatic biodiversity. It is mainly used in the studying of fish species diversity and has also been gradually used in the studying biodiversity of zooplankton and phytoplankton in recent years. This review firstly introduced the eDNA metabarcoding technique and its sampling method, and then focused on the application of this technique in the studying of biodiversity of zooplankton and phytoplankton to promote the development of eDNA metabarcoding technique in plankton diversity research.