Among the most enduring ecological challenges is an integrated theory explaining the latitudinal biodiversity gradient, including discrepancies observed at different spatial scales. Analysis of Reef Life Survey data for 4127 marine species at 2406 coral and rocky sites worldwide confirms that the total ecoregion richness peaks in low latitudes, near +15°N and −15°S. However, although richness at survey sites is maximal near the equator for vertebrates, it peaks at high latitudes for large mobile invertebrates. Site richness for different groups is dependent on abundance, which is in turn correlated with temperature for fishes and nutrients for macroinvertebrates. We suggest that temperature-mediated fish predation and herbivory have constrained mobile macroinvertebrate diversity at the site scale across the tropics. Conversely, at the ecoregion scale, richness responds positively to coral reef area, highlighting potentially huge global biodiversity losses with coral decline. Improved conservation outcomes require management frameworks, informed by hierarchical monitoring, that cover differing site- and regional-scale processes across diverse taxa, including attention to invertebrate species, which appear disproportionately threatened by warming seas.