There is increasing evidence that some of the spatial variation in characteristics of local assemblages of reef fish can be explained by variation in the measurable features of the habitat. In lagoons at Moorea, French Polynesia, the coral, Porites rus forms large, structurally complex patch reefs with surface branches and numerous holes and interior cavities. We conducted visual surveys of the fishes associated with a set of 66 P. rus patch reefs and recorded the microhabitat (branch, crevice, interior cavity, water column, etc.) where each fish occurred. In total, 119 species of fish from 25 families were observed in 17 pre-specified microhabitats. The families displayed a range of patterns of occurrence among the microhabitats with some (e.g., Gobiidae, Scorpaenidae) restricted to only a few types, while others (e.g., Apogonidae, Labridae) occurred in a variety of microhabitat types. Similarly, some microhabitats were numerically dominated by individuals within a single family (e.g., Apogonidae in crevices) and other microhabitats (e.g., branches, cavities) were occupied by individuals from numerous families. Knowledge of patterns of microhabitat use can provide useful predictive insight into likely alterations in the composition and structure of coral associated fishes resulting from changes in coral structure that can occur via growth, mortality and/ or damage.