This study aimed to fill the gap of knowledge on this group of fishes by estimating the natural stock, species composition and biodiversity of target reef fishes from three regencies; Alor, East Flores (Flores Timur) and Southwest Maluku (Maluku Barat Daya/MBD) using underwater visual census method. A total of 176 species belong to 19 families of economically important target fish were recorded from 62 survey sites. The highest estimated stock is located in Southwest Maluku Regency – based on both abundance and biomass values, followed by Alor Regency and the lowest in East Flores Regency. Target fish species from the family of Caesionidae has the highest composition both based on abundance (74%) and biomass (40%). The highest species composition of target fish is from Pterocaesio tile (57.65%) which is more than 50% of the overall target fish. Community structure of target fish in the three regencies is still in a relatively good condition based on diversity index (H’), evenness (E) and no domination (C) of a single species occurs inside the target fish community, with exception in Alor Regency where the community of target fish is indicated to be under pressure. Biodiversity index by Bray-Curtis analysis in each location shows that most of the sites have the similarity of 67.51%, suggesting that there is not much difference in terms of target fish community structure between the three regencies.