Abstract. Tropical reefs encompass tremendous biodiversity yet are imperiled by increasing natural and anthropogenic disturbances worldwide. Meiobenthic biota on coral reefs, for example, ostracods, may experience substantial diversity loss and compositional changes even before being examined. In this study, we investigated the reefal ostracod assemblages from the highly diverse and productive ecosystem in the Zanzibar Archipelago (Pemba, Zanzibar, and Mafia islands), Tanzania, to understand how their diversity and faunal structure vary in response to water depth, benthic community type, and human impacts. We characterized four distinct ostracod faunas associated with different benthic habitats, which were deep fore reefs, shallow fringing reefs, degraded fringing reefs, and algae-covered intertidal flats. We identified typical ostracod associations, i.e., Bairdiidae versus Loxoconchidae–Xestoleberididae, that showed affinities towards hard corals or algae on the reef platforms, respectively. The highest diversity was found on shallow fringing reefs where coral-affined and algae-affined taxa exhibited maximum overlap of their distributional ranges, while the sand flats, mangrove, and marginal reefs within the intertidal zone had much lower diversity with a high dominance of euryhaline taxa. Along the western coast of Zanzibar Island, coastal development likely resulted in a unique faunal composition and comparatively low diversity of ostracod assemblages among those in reefal habitats, in conjunction with overall reef ecosystem degradation. This study represents the first large-scale assessment of shallow-marine ostracods in the Zanzibar Archipelago. It lays a solid foundation for future research into the ecological significance of ostracods on coral reefs.