South Africa urgently requires a national strategic plan for the conservation of the country's biodiversity. The formulation of such a plan would be relatively easy if centres (hotspots) of richness, endemism and rarity were congruent, both within and among many different taxa, if these hotspots captured a large proportion of the total species, and if hotspots fell within existing reserves. The investigation of six vertebrate taxa (viz freshwater fish, frogs, tortoises and terrapins, snakes, birds, and various mammal orders) at a national scale reveals that hotspots are not coincident within taxa. Centres of richness are concentrated in the north-eastern areas of the country, whereas endemism is concentrated in the south-west, and centres of rare and threatened (Red Data Book) species can be in either area. Paired comparisons among taxa reveal greatly varying proportional overlaps of species richness hotspots (0-72%). The proportion of total species falling in hotspots ranges from low (66% for fish) to high (92% for birds). Hotspots are thus not an efficient method of siting representative (ideal) reserves. In order to design a more representative reserve system to protect all vertebrate species, a complementarity algorithm was applied to all taxa separately, and then to all taxa combined. The combined analysis yielded more efficient results (66 reserves are required to represent all 1074 species at least once) than the separate analyses (97 reserves). Many of these representative reserves coincide with both hotspots and existing reserves, and over 85% of the hotspots of most taxa coincide with existing reserves, thus South Africa's vertebrate fauna could be more effectively protected with only moderate acquisition of new, well-sited reserves. A biome analysis reveals that these reserves will also have to incorporate areas of those biomes that are currently inadequately protected, viz grassland, Succulent Karoo and Nama-Karoo. The methods outlined in this paper should be applied to as many other taxa as possible, in order to aid the formulation of a national strategic plan for biodiversity conservation.