Top predators are a critical part of healthy ecosystems. Yet, these species are often absent from spatially isolated habitats leading to the pervasive view that fragmented ecological communities collapse from the top down. Here we study reef fish from coral reef communities across the Pacific Ocean. Our analysis shows that species richness of reef fish top predators is relatively stable across habitats that vary widely in spatial isolation and total species richness. In contrast, species richness of prey reef fish declines rapidly with increasing isolation. By consequence, species-poor communities from isolated islands have three times as many predator species per prey species as near-shore communities. We develop and test a colonization-extinction model to reveal how larval dispersal patterns shape this ocean-scale gradient in trophic structure.