Coral reef fish are increasingly under pressure from habitat degradation, overfishing, and other stressors driven by climate change and human activities, and understanding how coral reef health and human disturbances impact fish community structure and assembly is essential for effective fisheries management and ensuring the sustainable supply of blue food. In this study, we collected fish environmental DNA (eDNA) from 48 coral reef sites across the Zhongsha, Xisha, and Nansha Archipelagos in May 2023, and these sites were grouped according to reef health and level of anthropogenic disturbance to analyze the effects of reef condition and anthropogenic activities on fish communities. The average of 119,954 reads were obtained after amplification using MiFish primers, and a total of 26,655 Molecular Operational Taxonomic Units (MOTUs) were recovered from samples. Although no significant differences in diversity indices were observed (p > 0.05), PERMANOVA revealed significant differences (P < 0.01) in both taxonomic and phylogenetic diversity across different coral reef conditions and levels of human disturbance, which might suggest that fish community composition in the Zhongsha, Xisha, and Nansha Archipelagos is shaped by the combined effects of habitat condition, human activity, and geographic factors. Further analysis of community assembly showed that fish communities in areas with excellent coral reef health and low human disturbance experienced stronger dispersal limitations, with relative importance values of 52.8% and 51.6%, respectively. This suggests that healthier reefs may provide diverse habitats, promoting local adaptation and self-recruitment. Ecological network analysis based on MOTU revealed that fish communities in healthier reefs exhibited more complex network links, supporting greater ecosystem stability. Network analysis indicates that deteriorating reef conditions may lead to the degradation of fish community structure and reduced biological interactions, potentially undermining fisheries productivity and the resilience of blue food systems. This study highlights the significant influence of coral reef health and human activities on the composition and structure of fish communities, providing essential data to inform regional fisheries management strategies and support blue food security.

coral reef fishery,community assembly,human disturbance,eDNA