Surveys of anemonefishes (Amphiprioninae) were conducted on reefs in two regions of the Great Barrier Reef Marine Park with contrasting histories of disturbance to determine the degree to which spatial variation might be explained by bleaching or management status. Densities of anemonefishes were lower on reefs in the bleaching-impacted Keppel Islands than on reefs in Far North Queensland. No anemonefishes or anemones were found on or near bleached corals in the Keppel Islands. Furthermore, the highest densities of fishes were found on reefs closed to fishing and aquarium collecting in both the Keppel Islands and Far North Queensland, which suggests that collecting is compounding the effects of bleaching. These results emphasize the importance of understanding the interaction between bleaching events and anthropogenic disturbance upon commercially exploited species.