Fisheries exploitation provides the opportunity to examine the ecosystem-scale biodiversity consequences of predator removal. We document predatory reef fish densities, coral-eating starfish densities and coral reef structure along a 13-island gradient of subsistence exploitation in Fiji. Along the fishing intensity gradient, predator densities declined by 61% and starfish densities increased by three orders of magnitude. Reef-building corals and coralline algae declined by 35% and were replaced by non-reef building taxa (mainly filamentous algae), as a result of starfish predation. Starfish populations exhibited thresholds and Allee-type dynamics: population growth was negative under light fishing intensities and high predator densities, and positive on islands with higher fishing intensities and low predator densities. These results suggest the depletion of functionally important consumer species by exploitation can indirectly influence coral reef ecosystem structure and function at the scale of islands.