Aliwal Shoal is a subtropical, algal-dominated reef in a marine protected area located south of Durban, South Africa. The shoal has historically been heavily utilized by fishermen and SCUBA divers. In this study, a survey was undertaken to describe and zone the reef and its benthic communities in terms of topography, habitat types, species diversity, species richness and benthic cover. Data were collected using underwater photography and analysed by point intercept analysis. Three distinct benthic communities were identified using multivariate non-metric statistics. Benthic communities appeared to be influenced by topography, sediment cover and wave energy. The highest abundance of zooxanthellate hard corals and the encrusting zooxanthellate sponge, Suberites kelleri were found on the large shallow areas of the shoal. This suggested that light penetration to the elevated areas on the reef was adequate for photosynthesis and played a role in the distribution of its biota. The encrusting morphology of the sponge Suberites kelleri, and the branching morphology of the hard corals Stylophora pistillata and Pocillopora spp., appeared to be tolerant of the high-energy environment near the surface. A second community was found only on steep edges of the Shoal and was characterized by a large abundance of Polychaeta and the soft coral Eleutherobia aurea, while a third community was found deeper on the offshore side of the shoal and consisted primarily of coralline and red foliose algae.