Abstract: Reef-associated organisms play a vital role in maintaining the stability of coral reef ecosystems by participating in key ecological processes such as energy flow, material cycling, and interspecific interactions. Therefore, investigating the community structure and diversity of reef organisms, as well as monitoring the distribution and temporal dynamics of key biological groups, is fundamental to understanding coral reef ecosystems. In this study, environmental DNA (eDNA) metabarcoding targeting the COI gene was employed to analyze 127 seawater and sediment samples collected from the shallow and mesophotic zones of coral reefs in the Xisha Islands. The results revealed that reef-associated organisms in these coral reefs were annotated to 14 phyla, 32 classes, 111 orders, 379 families, 625 genera, and a total of 901 metazoan species. Among them, Mollusca accounted for the highest proportion with 217 species, followed by Arthropoda with 186 species. Although there was little difference in the overall biodiversity of Mollusca and Arthropoda between shallow and mesophotic habitats, their community structures differed significantly, exhibiting a clear vertical distribution pattern within the coral reef ecosystem. Additionally, the biodiversity of reef-associated organisms detected in seawater samples was significantly higher than that in sediment samples, with only 136 species identified from sediments, highlighting that sediment eDNA serves as an important complement in assessing reef-associated biodiversity. This study demonstrates that, compared to traditional morphological surveys, eDNA metabarcoding offers a more comprehensive approach for revealing the biodiversity and spatial distribution patterns of reef-associated organisms in coral reef ecosystems.

Key words: Mesophotic coral ecosystems, Environmental DNA, Mollusca, Arthropoda, Biological Diversity