Species commonly associate with habitat structures that afford protection from predators. The quality of such refuges may be influenced by a variety of factors, including size and setting in the local habitat as well as the set of interactions that occur within the structures themselves. We explored whether these factors influenced the efficacy of a structural refuge for tropical reef fish. The refuge was the common branching coral Pocillopora eydouxi, which harbors a suit of species of fishes and trapeziid crabs on reefs in Moorea, French Polynesia. Survey data indicated that corals harboring the red-spotted coral crab (Trapezia rufopunctata) and/or predatory hawkfish (Cirrhitidae) had half the density of resident fish than corals lacking those two groups. A field experiment tested whether red-spotted coral crabs affected the mortality of young yellowtail dascyllus (Dascyllus flavicaudus) and assessed whether the influence of coral crabs depended on the presence of older conspecific fish. The experiment revealed that both coral crabs and older conspecifics increased mortality, but that their joint effects on mortality were additive. In addition, both slight variation in size of the shelter coral and its distance (within 6 m) from the nearest natural patch reef (a local source of predators) affected mortality of young dascullus. These findings (1) demonstrate that interactions among taxonomically disparate species can play a substantial role in shaping patterns of abundance and (2) highlight the fact that the quality of a shelter microhabitat can be influenced substantially by very fine-scale variation in its size and settings as well as by the combination of organisms that occupy it.