Conservation planning has hitherto concentrated largely on the representation of biodiversity patterns within a system of conservation areas. Only recently has there been an emphasis on retaining segments of the optimal conservation area by defining implementation priorities in terms of the irreplaceability of areas and their vulnerability to threatening processes. The conservation of ecological and evolutionary processes that sustain and generate biodiversity, a requirement for a system of conservation areas that promotes biodiversity persistence, has received very little attention. By designing conservation systems in order to represent spatial features as surrogates for ecological and evolutionary processes, and by scheduling the implementation of areas in order to minimise the impacts of threats on these processes, it is theoretically possible to achieve a conservation system that combines retention and persistence. Here we discuss the requirements for establishing a sustainable (retention+persistence) conservation system in southern Africa's Succulent Karoo, a mediterranean-climate desert that is very rich in plant species. Firstly, we discuss planning issues salient to both representation and design, and indicate the location, size and role in conservation of the spatial components (surrogates for processes) necessary for a system of conservation areas in the Succulent Karoo intended for retention+persistence. Next we lay out the requirements for a conservation system in the region and summarise some existing work on representation and retention of plant species. We then present a protocol for decision-making and apply it by designing a hypothetical system of conservation areas. Finally, we compare representation of Red Data Book plant species in a system identified for pattern retention with our similar-sized system designed for retention+persistence. The latter conserves 37% fewer species, indicating that design for persistence incurs a cost in terms of representation. This cost is offset by developing a conservation system that is likely to persist in the face of global change, and that will sustain processes responsible for the maintenance and genesis of biodiversity.