A study on coral reefs status was conducted on the island of Wetar, Leti, and Moa of Southwest Maluku District. Nine stations were assigned as sampling stations to analyze the coral reefs' condition of these three islands. The Underwater Photo Transect method was applied to analyze the percentage of biotic and abiotic components of coral reef communities with Coral Point Count Excel (CPCe) software, whilst the underwater visual census for reef fish data. Coral reef health indices were determined based on benthic lifeform components and reef fish biomass. Our findings showed that the coral cover in Wetar, Moa, and Letti island consists of 124 species that belong to 44 genera and 15 families of hard coral. The condition of coral reefs was considered at category 3 due to the high percentage of coral cover that range between 20.85–71.55% with an average of 42.87%. The average biomass of target fish in the waters of Wetar, Letti, Moa, and its surrounding areas was 129.309 g/m2 or 3,694 kg/ha. The Kaiwatu site (BWI03) was recorded to have the highest biomass of 305,487 g/m2 or 8,728 kg/ha and the lowest was the Klis site ((BWI 08) with a value of 1285 g/m2 or 36, 70 kg/ha. The coral reef health index values of nine study sites ranged between grade 5 and 10, of which two locations got a score of 10 (very good) categories, five locations got a good category and two locations got a low score. The overall results indicate that the coral reef is in a healthy condition, yet, the use of non-environmental friendly fishing gears partly damages coral reef beds.