In the past few years, environmental DNA (eDNA) techniques have been used to monitor marine communities. Research indicates that eDNA is an effective tool for monitoring fishery resources. This study analyzed the seasonal variations in fish resources in the Yangtze Estuary, China, using eDNA. A total of 103 water samples were collected from the Yangtze Estuary across the four seasons in 2019—20 samples in February, 28 in May, 28 in August and 27 in November. Our research successfully detected the fishery resources of the Yangtze Estuary. We found significant differences according to the season. The results showed that 59 species were identified in 2019 (20 in February, 16 in May, 5 in August and 45 in November) and fish species varied widely over the four seasons. Furthermore, our samples revealed significant differences in annual fish stocks in the Yangtze Estuary, compared with eDNA data from 2018 and with traditional surveys from past years. Overall, eDNA is a useful emerging tool to assist with monitoring and protecting fish resources for the Yangtze Estuary.
