Abstract: Environmental DNA (eDNA) is a booming biological monitoring technology. It has been proved by many studies to be an effective tool for the detection, monitoring and indication of fish species and its biodiversity and abundance. This study applies high-throughput sequencing technology to analyze the eDNA samples of the waters of the Yangtze Estuary and compares the results with the traditional fishery studies. It aims to elaborate the diverse characteristics of the fish communities in the Yangtze Estuary and to explore the prospects of applying eDNA technology to the diversity study of the fish species in the Yangtze Estuary. The study results show that the eDNA detects 45 fish species, which can be classified to 41 genera, 21 families and 10 orders, and there is no significant difference of the abundances of the species, but their diversity characters vary considerably, while the bottom trawl method detects 33 fish species, which can be classified to 29 genera, 16 families and 11 orders. 18 species, accounting for 30% of the total fish species, can be detected in both monitoring methods. Among those 18 species, the number of Perciformes is the most, followed by Cypriniformes. The results of both monitoring methods show Coilia nasus and Coilia mystus are the dominant species in the Yangtze Estuary. When comparing the two monitoring methods by Alpha diversity, both Simpson and Shannon indexes show the Alpha diversity of the fish communities in the Yangtze River Estuary detected by eDNA method is significantly greater than of bottom trawl. The study shows that it is feasible to apply eDNA technology in monitoring fishery resources in the Yangtze River Estuary, while during the fishing moratorium different methods can be used to monitor fishery resources based on the actual situation.