Daya Bay is a provincial aquatic resources nature reserve, which is not only rich in biological resources, but also an important spawning and feeding ground for many economic fishes (Fig. 1). In order to protect the fishery resources of Daya Bay, four otter trawl surveys of fishery resources were conducted in April (spring), August (summer), October (autumn) and December (winter). Combining distance to the nearest mainland, distance to the nearest larger island, water depth, water temperature, salinity, chlorophyll a, total nitrogen, total phosphorus, maximum standard length of fish and catch per unit of effort, we discussed the nested patterns of fish assemblages in Daya Bay and its influencing factors (Appendix, Table 1). The result showed that the community composition of fishes in Daya Bay was significantly nested. The maximum standard length was significantly associated with their nested matrix ranks (Table 3), indicated that selective colonization was the main driver of nestedness of fishes in Daya Bay. All year round, the fish in Daya Bay tend to choose to inhabit the sea areas of Yangmeikeng and northern Dalajia Island (Table 2). This suggested that the sea areas of Yangmeikeng and northern Dalajia Island were the main distribution areas of fish. The Yangmeikeng was the main fattening area of fish, and the sea area of northern Dalajia Island was the fish spawning ground, both sea areas should pay prior attention to protection and management, moreover, both were the most suitable sites for fishery stock enhancement.