Theory predicts that loss of gape-limited sharks should lead to increases in the abundance and biomass of smaller size classes of prey. We used stereo-baited remote underwater video stations (stereo-BRUVS) and stereo diver-operated video systems (stereo-DOVS) to characterise the shark and fish assemblages on 2 remote, atoll-like reef systems in northwestern Australia, the Rowley Shoals and the Scott Reefs. Whereas the Rowley Shoals is a marine protected area, sharks have been removed from the Scott Reefs for over 3 centuries. We found that sharks were significantly more diverse, more abundant, larger in size and greater in biomass in the marine reserve relative to the Scott Reefs. Consistent with a priori hypotheses, bony fishes displayed greater species diversity, abundance and biomass where sharks were common relative to the predator-depleted location. The size and trophic structure of bony fish assemblages also differed between locations. Our results provide large-scale evidence consistent with the hypothesis that reef-associated sharks are gape-limited trophic omnivores that impose top-down effects on medium sized (<50 cm), low- to mid-trophic level fishes. On stereo-BRUVS, for example, prey in the 0 to 29.99 cm size class had 203% more biomass at the predator-depleted reef relative to the location where sharks were abundant. As body size is an important determinant of ecological role and fitness in fishes, these findings suggest that the rapid and ongoing loss of sharks from reefs globally may have important implications for reef management and investigations into the effect of fishing on reef systems.