The analysis of coral community structure and diversity by means of line transects provides a powerful tool for reef management. In South Africa, this approach was used to develop a zoning scheme for the Maputaland and St Lucia Marine Reserves. Coral communities differed between reefs. Shallow reefs were dominated by Alcyonacea of the genera Lobophytum and Sinularia. Tissue regeneration experiments suggested that these corals were able to survive lesions, which can be inflicted, for example, by careless divers or by anchoring, so no special protection was considered necessary. Deep reefs were dominated by Scleractinia of the genus Acropora. Monitoring of breakage and fragment survival experiments indicated that the dominant species in this community were easily damaged and therefore special protection is needed. Sanctuary areas are proposed in diverse upstream reefs to serve as larval reservoirs in case degeneration occurs downstream.