Coral reef fishes perform a range of vital ecosystem functions, and can serve as indicators of ecological stress and resilience. However, many species are not observed when using Underwater Visual Census (UVC) during biomonitoring, and therefore overall biodiversity is often underestimated. Environmental DNA (eDNA) is proposed as an advanced and non-invasive next-generation biomonitoring method for determining the presence of aquatic organisms such as fish. Therefore, this study aimed to assess the community structure of coral fish from three different marine protected area reef zones (utility zone, open access zone, core zone) around Lombok Island using eDNA metabarcoding. Biological community composition, richness, and diversity were evaluated based on reads from mid-column water and sediment samples. A total of 58 species were identified from the eDNA samples using the Multiplex Barcode Research And Visualization Environment (mBRAVE) pipeline. The Shannon–Wiener index (H') showed significantly higher species diversity in the core zone than the utility and open access zones. There was no significant between-zone difference in community structure (ANOSIM, R = 0.11 < 0.25). NMDS analysis using the Bray–Curtis test showed significant between-zone differences in species diversity and abundance (PERMANOVA Adonis Pr (> F) = 0.001, p < 0.05). Based on the high number of fish species detected in this study, eDNA can be recommended as an alternative tool or as a complement to visual survey methods for biological monitoring and diversity assessment of remote reefs, with less stringent requirements in terms of field conditions (e.g. visibility) and taxonomic expertise.

珊瑚礁鱼类具有一系列重要的生态系统功能，可作为生态压力和恢复力的指标。然而，在生物监测过程中使用水下视觉普查 (UVC) 时没有观察到许多物种，因此整体生物多样性往往被低估。环境 DNA (eDNA) 被提议作为一种先进的、非侵入性的下一代生物监测方法，用于确定鱼类等水生生物的存在。因此，本研究旨在使用 eDNA 元条形码评估龙目岛周围三个不同海洋保护区珊瑚礁区（实用区、开放区、核心区）的珊瑚鱼群落结构。根据中柱水和沉积物样本的读数评估生物群落组成、丰富度和多样性。使用多重条码研究和可视化环境 (mBRAVE) 管道从 eDNA 样本中鉴定了总共 58 个物种。Shannon-Wiener 指数 (H') 显示核心区的物种多样性明显高于公用事业区和开放区。群落结构没有显着的区间差异（ANOSIM，R = 0.11 < 0.25）。使用 Bray-Curtis 检验的 NMDS 分析显示物种多样性和丰度的显着区域间差异（PERMANOVA Adonis Pr (> F) = 0.001，群落结构没有显着的区间差异（ANOSIM，R = 0.11 < 0.25）。使用 Bray-Curtis 检验的 NMDS 分析显示物种多样性和丰度的显着区域间差异（PERMANOVA Adonis Pr (> F) = 0.001，群落结构没有显着的区间差异（ANOSIM，R = 0.11 < 0.25）。使用 Bray-Curtis 检验的 NMDS 分析显示物种多样性和丰度的显着区域间差异（PERMANOVA Adonis Pr (> F) = 0.001，p  < 0.05)。基于本研究中检测到的大量鱼类，可以推荐 eDNA 作为替代工具或作为对偏远珊瑚礁生物监测和多样性评估的视觉调查方法的补充，对野外条件的要求不太严格（例如可见性）和分类学专业知识。