Investigation of most ecological patterns and processes involves convenient daytime sampling, with little consideration of the contributions of nocturnal taxa, particularly in marine environments. Here we assess diel partitioning of reef faunal assemblages at a continental-scale utilizing paired day and night visual census across 54 shallow tropical and temperate reefs around Australia. Day/night differences were most pronounced in the tropics, with fishes and invertebrates displaying distinct and opposing diel occupancy on coral reefs. Tropical reefs in daytime were occupied primarily by fishes not observed at night. By night, substantial emergence of invertebrates not otherwise detected during sunlit hours occurred. Nocturnal emergence of tropical invertebrates corresponded with significant declines in the richness and biomass of predatory and herbivorous diurnal fishes. In contrast, relatively small diel changes in fishes active on temperate reefs corresponded to limited nocturnal emergence of temperate invertebrates. This reduced partitioning suggests fish communities may impart strong top-down pressures on invertebrate communities, either by predation or competitive interference, and thus regulate invertebrate activity/density, at least in part. For shallow reefs, the diel cycle triggers distinct emergence and retreat of faunal assemblages and associated trophic patterns and processes, which otherwise go unnoticed during hours of regular scientific monitoring.