Species names and geographic ranges form the basis of biodiversity science and help inform conservation policy. As such, un-named, un-described and unresolved species are not accounted for in conservation research. Here we use a phylogenomic dataset of >2500 conserved loci for 881 staghorn corals (Acropora) collected from 24 locations across the Indo-Pacific to highlight the extensive hidden diversity on coral reefs. We identify over 250 ‘primary species hypotheses’, of which only ~30% can be confidently assigned to a nominal species. The remaining lineages represent species that are either currently in synonym, unresolved or undescribed. A geographic assessment of currently accepted species that our phylogenomic analyses resolve shows little overlap in coral assemblages between biogeographic regions across the Indo-Pacific and along the Great Barrier Reef. As a consequence, lineages thought to be geographically widespread have much narrower distributions, particularly at peripheral locations. Our findings have important implications for understanding contemporary biodiversity patterns on coral reefs, connectivity among reef bioregions and the outcomes of proposed conservation and intervention measures. Given the increasing spatial footprint and severity of disturbances on reefs globally, the high proportion of hidden diversity for corals highlights the urgent need for accurate information on the identity and distribution of these key ecosystem engineers.