Since 2010, Marine Protected Areas (MPAs) have been established in Indonesia to ensure the sustainable management of coral reef ecosystems. This study examines fish assemblages across varying depths and MPAs management areas, specifically assessing the suitability of Gili Rakit and Gili Lipan MPAs. The study concludes that deeper coral reefs have higher reef fish abundance, with a majority of carnivores, planktivores, and omnivores. Gili Taekebo has the lowest abundance and species richness, while Pulau Lipan has the highest. The target reef fish are primarily found in the core zone, rehabilitation, and open access management types. Based on the findings, MPAs should prioritize sites with gradient depth coral reefs and complex habitats to enhance reef fish biodiversity richness. Takad Tabampang and Pulau Bedil are recommended as sustainable fisheries management types, while Gili Taekebo could benefit from rehabilitation or open access management. Pulau Lipan and Labajo may benefit from target fish re-stocking programs.