A fishery independent underwater visual census technique was used to assess the effects of fishing on the diversity, biomass and trophic structure of the diurnally active non-cryptic reef-associated fish communities of the Seychelles. One hundred and thirty four species associated with three significantly different types of reef habitat were censused at one unfished ground and in six fishing grounds subject to different fishing intensities. There was in inverse relationship between fishing intensity and the biomass of several species targeted by the fishery. The diversity of families containing target species (lutjanidae, lethrinidae) was significantly higher at unfished and lightly fished sites as was the total biomass of the fish community and the biomass of piscivorous, piscivorous/invertebrate feeding and herbivorous trophic groups. However, there was no indication that the biomass of non-target species increased in response to the removal of their predators by fishing. The findings of this study are significant for fishery managers because they suggest that the intensive differential cropping of top predators will not necessarily lead to increases in the biomass and productivity of their prey.