The importance of studying coral communities at different spatial scales is acknowledged in a growing volume of scientific literature, and principles of landscape ecology were thus used to elucidate the patterns in coral community structure on the high-latitude reefs in South Africa. These reefs are at the southernmost distribution of this fauna in Africa, are surprisingly species rich, and represent a biodiversity peak in this fauna south of the equator, regardless of the marginal nature of the environment. Coral community patterns were identified on and between the reefs at Sodwana Bay, justifying the grouping of reef areas in distinct zones. A number of landscape components were identified, ranging from the entire reef complex (10 km scale), individual reefs (1 km scales) and reef zones, to components that were separated using multivariate statistical analysis of transect data. These components transcended spatial similarities, e.g. the fore-reef on Five-mile Reef was not similar to the fore-reef on Seven-mile Reef, but was rather grouped with the reef flat on Two-mile Reef. This information was “translated” into an index of management intervention, based on risk assessment, and was generated using parameters that measure susceptibility to crown-of-thorns feeding, bleaching, diver-related damage and swell-induced breakage. We also assessed was the time elapsed since the last major disturbance and the proximity to the only boat launch site, a proxy measure of continuous disturbance. The risk assessment suggested that conservation management is most needed in the stable and “climax” coral communities that are usually characterised by a near-equal mix of hard and soft corals at maximal coral species diversity.