LAUSR

Simple Summary With the development of molecular techniques, environmental DNA (eDNA) methods are increasingly being applied to assess marine fish biodiversity. Fish biodiversity survey methods have been difficult to standardize due to the diversity and complexity of reef habitats. Traditional surveys can damage island ecosystems. A rational method for surveying fish biodiversity in different habitats is urgently needed. This study aimed to investigate the practical validity of the eDNA method for evaluating the fish composition and diversity in different habitats. Additionally, compared with traditional surveys, the eDNA method includes the same results, but also includes species that would not be caught by traditional surveys due to the technical limitations of traditional surveys. This is significant for continuous biodiversity monitoring and management in protected areas. Abstract This study aimed to investigate the practical validity of the environmental DNA (eDNA) method for evaluating fish composition and diversity in different habitats. We evaluated the fish composition and diversity characteristics of seven different habitats in the Ma’an Archipelago Special Protected Area in April 2020. The results showed that a total of twenty-seven species of fishes belonging to six orders, eighteen families, and twenty-three genera of the Actinopterygii were detected in the marine waters of the Ma’an Archipelago Special Protected Area. The dominant species in each habitat were Larimichthys crocea, Paralichthys olivaceus, and Lateolabrax maculatus. The mussel culture area had the highest number of species, with 19 fish species, while the offshore bulk load shedding platform had the lowest number of species, with 12 fish species. The rest of the habitat was not significantly different. The results showed that the mussel culture area had the highest diversity index (average value of 2.352 ± 0.161), and the offshore bulk load shedding platform had the lowest diversity index (average value of 1.865 ± 0.127); the rest of the habitat diversity indices did not differ significantly. A comparison with historical surveys showed that the eDNA technique can detect species not collected by traditional methods such as gillnets and trawls. Our study demonstrates the role of eDNA technology in obtaining fish diversity in different habitats and provides a theoretical basis for the continuous monitoring and management of fish biodiversity in protected areas.