On land, biodiversity hotspots typically arise from concentrations of small-range endemics. For Indo-Pacific corals and reef fishes, however, centres of high species richness and centres of high endemicity are not concordant. Moreover ranges are not, on average, smaller inside the Central Indo-Pacific (CI-P) biodiversity hotspot. The disparity between richness and endemicity arises because corals and reef fishes have strongly skewed range distributions, with many species being very widespread. Consequently, the largest ranges overlap to generate peaks in species richness near the equator and the CI-P biodiversity hotspot, with only minor contributions from endemics. Furthermore, we find no relationship between the number of coral vs. fish endemics at locations throughout the Indo-Pacific, even though total richness of the two groups is strongly correlated. The spatial separation of centres of endemicity and biodiversity hotspots in these taxa calls for a two-pronged management strategy to address conservation needs.