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Apex predators are known to exert strong ecological effects, either through direct or indirect predator–prey interactions. Indirect interactions have the potential to influence ecological communities more than direct interactions as the effects are propagated throughout the population as opposed to only one individual. Indirect effects of apex predators are well documented in terrestrial environments, however there is a paucity of information for marine environments. Furthermore, manipulative studies, as opposed to correlative observations, isolating apex predator effects are lacking. Coral reefs are one of the most diverse ecosystems, providing a useful model system for investigating the ecological role of apex predators and their influence on lower trophic levels. Using predator models and transplanted macroalgae we examined the indirect effects of predators on herbivore foraging behaviour. We show that the presence of a model reef shark or large coral-grouper led to a substantial reduction in bite rate and species richness of herbivorous fishes and an almost absolute localized cessation of macroagal removal, due to the perceived risk of predation. A smaller-sized coral-grouper also reduced herbivore diversity and activity but to a lesser degree than the larger model predators. These indirect effects of apex predators on the foraging behaviour of herbivores may have flow-on effects on the biomass and distribution of macroalgae, and the functioning of coral reef ecosystems. This highlights that the ecological interactions and processes that contribute to ecosystem resilience may be more complex than previously assumed.