Marine reserves can directly replenish heavily fished species. However, community-wide effects of reserves are less clear. Marine reserves directly reduce fishing mortality rates, but through the restoration of apex predators, reserves may have strong indirect effects on non-target species. We explored the effects of a large, fully protected marine reserve in the Bahamas on the community of coral-reef fishes. We examined the effect of the reserve on fish biomass by comparing the density and size of all fishes on similar reefs located inside and outside the reserve. Total biomass of fishes was approximately 7× higher in reserve sites, where biomass was strongly concentrated in species of higher trophic levels. Analysis based on the relative magnitude of individual species’ responses indicated that, on average, the largest species increased in biomass within the reserve, intermediate-sized species decreased, and the smallest species exhibited variable responses. Species’ responses to the reserve were also examined by pooling species into 9 trophic categories using consumptive relationships, which provided corroborating results. Large piscivores (e.g. sharks, large groupers) were on average larger and more abundant inside the reserve. Mid-trophic-level groups (e.g. small piscivores) had higher average biomass outside of the reserve, where the number of species and biomass of large predators was lower. Finally, some low-trophic-level groups (e.g. planktivores) had higher biomass within the reserve, while others (e.g. small herbivores) did not respond strongly. Overall, these results suggest that marine reserves can substantially alter the composition and structure of reef fish communities.