Wuzhizhou Island (WZZ) is one of the most mature tourism islands on the coast of the South China Sea, and its surrounding waters are rich in tropical coral reef fishes. Tourism could affect marine biodiversity, especially the coral reef fish community. In order to understand the species diversity of fish surrounding WZZ, environmental DNA (eDNA) samples were collected from six sampling sites around the island, located in the core and non-core tourism areas, respectively, from 2022 to 2023. In total, 188 fish species, belonging to 124 genera, 63 families and 17 orders, were detected using eDNA method. The Perciformes contained the highest number of species (n = 130, 69.15% of total number). Compared to traditional fishing nets, eDNA could provide more information on fish species. The results indicated that species richness and Margalef’s index were higher at the sampling sites in the core area of tourism of WZZ, which maybe relevant to tourism-based provisioning. By contrast, the Shannon–Wiener index, Pielou’s index and dominant species of fish did not display significant differences between core and non-core tourism areas. On the basis of the results of the β-diversity index, the differences in fish communities had a closer relationship to geographical location. Furthermore, there were obvious differences in fish communities in different seasons, which may be attributed to the influence of ocean currents.

Spatial and Temporal Diversity of Fishes at Wuzhizhou Island in the South China Sea Based on Environmental DNA