Abstract: Microbial community, as a key link in the food chain, plays an important role in aquatic ecosystems, and its structure and function can well reflect the water quality characteristics in different habitats. “Water quality-Microbial community biomonitoring-PFU method” is the first national standard for biomonitoring system in China, and has proved to be a fast, economical and reliable. However, because the PFU method requires high professional knowledge, is time-consuming and power-consuming and not easy to standardize, it seriously hinders the application and dissemination of this method. In recent years, the rapid development of environmental DNA (eDNA) technology has broken the bottleneck of microbiological morphological identification of various aquatic organisms including microorganisms in the environment. We propose the microbial community biomonitoring eDNA-PFU method, which means that the PFU monitoring is improved by eDNA technology, as ecological assessment indicators for lakes, rivers and reservoirs. In order to verify the above proposal, we carried out pre-experiments on the monitoring of protozoan communities in the East Lake in Wuhan. The results showed that the eDNA-PFU method has higher coverage and sensitivity comparing with the traditional PFU method, and can reveal the structural characteristics of microbial community comprehensively and accurately. Therefore, microbial community biomonitoring based on the eDNA-PFU method is expected to provide a new generation of biomonitoring standards for the ecological assessment of water bodies such as lakes, rivers and reservoirs.