The biotic community at a shelf-edge reef, which abruptly delineates a continuous fringing reef from the adjacent mesophotic reef off southwestern Puerto Rico, USA, was used to identify patterns of differential habitat use in reef fishes. Our study used multivariate analyses to identify groupings within the fish community associated with this area. These groups were suggestive of differential habitat use by the fish community, in particular with respect to the reef-terrace vs slope locations. The benthic composition among these two location stratifications differed while remaining surprisingly consistent within each location strata (i.e., reef-terrace vs slope). The variability in both the fish and benthic communities was best explained in our model by the location stratifications within each site as opposed to the physical position of the site itself along the shelf edge. Food resources, structure (i.e., habitat complexity), or both may contribute to differential habitat use within the reef-fish communities observed. A lesser division was apparent within the reef-terrace locations that grouped the western samples separately from the eastern. The results presented in the present study suggest that the fish communities along the shelf-edge reef adjacent to La Parguera, Puerto Rico, are divided by habitat type and location as determined by food and shelter availability. Here, we present an analysis whereby community structure can be identified at varying spatial scales within a single depth zone to inform managers prior to strategy implementation.