In this study, we investigated the species composition and habitat use of black seabreams Acanthopagrus on the Okinawa Island based on the fishery data and available environmental information. Our findings revealed that at least two Acanthopagrus species are present as well as coexist in the coastal areas on the Island. Acanthopagrus chinshira predominantly inhabited the inner bay habitats of the island, specifically the tidal flats characterized by sandy–muddy or muddy sediments. Conversely, Acanthopagrus sivicolus demonstrated a wider range of habitat preferences, including not only the inner bay habitats but also seagrass beds, coral reefs, and fishing grounds with rivers. These findings suggest that A. sivicolus might be able to adapt to more diverse environments than A. chinshira. The stomach content analysis, categorized by seasonal and age classes, indicated that A. chinshira primarily fed on bivalves and gastropods (Cerithioidea). However, A. sivicolus was suggested to seasonally feed in an opportunistic manner on the snails of Cerithioidea superfamily and exhibited more varied diet than A. chinshira. Nakagusuku Bay emerged as the most notable landing area for these two black seabreams in all fishing grounds on Okinawa Island. However, the landings of these two black seabreams were predominantly concentrated in the Nakagusuku Bay during active spawning season from January to March; thus, their landings during this period were accounted for over 35% (average; A. chinshira: 69.9%, A. sivicolus: 60.8%) of their total annual landings in each of the past 27 years (from 1989 to 2015). The results of this study implied that A. chinshira, as a species with specific dietary and habitat requirements and a declining population, is plausibly more susceptible to vulnerabilities than A. sivicolus.