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Journal of Tropical Oceanography

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Summer diversity of mesophotic coral reef fishes and establishment of a DNA Barcoding Database in the Xisha islands

CHEN Xi1, 2, LIN Xianzhi3, 4, 5, LIN Lin6, 7, WANG Teng6, 7, LIU Yong6, 7, LIU Sheng 1, LING Daxiao1, 8, ZHOU Yanyan1, ZOU Keshu2, ZHANG Li 1, 4, 5    

  1. 1. State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China;


    2. College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China;


    3. Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China;


    4. National Field Observation and Research Station (Hainan Sanya) for Marine Ecosystem, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China


    5. Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572000, China;


    6. Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangdong Provincial Key Laboratory of Fishery Ecology Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China;


    7. Scientific Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/ Sanya Tropical Fisheries Research Institute, Sanya 572018, China;


    8. University of Chinese Academy of Sciences, Beijing 100049, China


  • Received:2026-03-20 Revised:2026-06-19 Accepted:2026-07-06
  • Supported by:

     Science & Technology Fundamental Resources Investigation Program (2022FY100600); Hainan Provincial Natural Science Foundation of China (423CXTD392); The program of State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences (SKLTO2025PT002); Science and Technology Planning Project of Guangdong Province, China (2023B1212060047); Special Project of the National Natural Science Foundation of China(L2424234)

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Abstract: Mesophotic coral reef ecosystems (MCEs) play a crucial role in global marine ecosystems. However, China lacks systematic surveys of mesophotic coral reef fishes, and no native DNA barcoding database for these fishes has been established to date. In this study, 465 fish individuals were collected at depths of 30–100 m from 9 core islets and reefs in the Xisha Islands in August 2024 through hand fishing and diving capture. A combination of morphological identification and mitochondrial Cytochrome c oxidase subunit I (COI) gene barcoding technology was employed to systematically analyze the characteristics of fish diversity in this region. A total of 83 fish species were identified, belonging to 1 class, 7 orders, 21 families, and 44 genera. Among the fish composition, Perciformes dominated absolutely (81.71%), small-sized fishes constituted the majority of the body size composition (40.96%), and carnivorous fishes accounted for as high as 96.38% of the feeding habits. Analysis of habitat depth showed that broadly distributed species made up 83.13%, confirming that mesophotic coral reefs are key transition zones connecting shallow and deep-water ecosystems. Phylogenetic analysis based on the COI gene revealed a distinct barcoding gap, and the mean posterior probability (PP) obtained from the bPTP (Bayesian Poisson Tree Processes) analysis was 0.80, supporting the reliability of species identification. This study is the first to systematically reveal the diversity characteristics of mesophotic coral reef fishes in the Xisha Islands and establish the first native DNA barcoding database for these fishes. It provides an important scientific basis for the conservation management and biodiversity monitoring of mesophotic coral reef ecosystems in the South China Sea.

Key words: Xisha Islands, Mesophotic Coral Ecosystems (MCEs), Fish diversity, DNA barcoding, COI gene, Community structure