Fish Community Composition and Seasonal Variation in the Coastal Waters of Sanya (Hainan, China) Based on eDNA Metabarcoding

To characterize the fish community composition and seasonal variation in the coastal waters of Sanya, a tropical coastal region on Hainan Island in the northern South China Sea, and to evaluate the applicability of environmental DNA (eDNA) metabarcoding for biodiversity monitoring, water samples were collected from 16 nearshore sampling sites in June 2024 and January 2025. Fish community structure was analyzed using eDNA metabarcoding, combined with diversity indices and multivariate statistical analyses. A total of 488 marine fish species were detected, including 426 species in summer and 205 species in winter, with higher species richness observed in summer. Perciformes was the dominant order in both seasons. Dominant species composition varied seasonally, with a relatively dispersed pattern in summer and a dominance concentration structure in winter. The Chao1 and Shannon indices were significantly higher in summer than in winter, whereas evenness showed no significant seasonal difference. NMDS and ANOSIM analyses revealed significant seasonal differences in community structure, and low Sørensen similarity coefficients indicated substantial species variation between seasons. These results indicate that fish communities in the coastal waters of Sanya exhibit clear seasonal variation. eDNA metabarcoding provides an effective complementary approach for monitoring fish diversity in complex coastal habitats, although its results may be influenced by eDNA transport, degradation, and reference database limitations.