Systematic conservation planning is a branch of conservation biology that s
eeks to identify spatially explicit options for the preservation of biodive
rsity. Alternative systems of conservation areas are predictions about effe
ctive ways of promoting the persistence of biodiversity; therefore, they sh
ould consider not only biodiversity pattern but also the ecological and evo
lutionary processes that maintain and generate species. Most research and a
pplication, however, has focused on pattern representation only. This paper
outlines the development of a conservation system designed to preserve bio
diversity pattern and process in the context of a rapidly changing environm
ent. The study area is the Cape Floristic Region (CFR), a biodiversity hots
pot of global significance, located in southwestern Africa. This region has
experienced rapid (post-Pliocene) ecological diversification of many plant
lineages; there are numerous genera with large clusters of closely related
species (flocks) that have subdivided habitats at a very fine scare. The c
hallenge is to design conservation systems that will preserve both the patt
ern of large numbers of species and various natural processes, including th
e potential for lineage turnover. We outline an approach for designing a sy
stem of conservation areas to incorporate the spatial components of the evo
lutionary processes that maintain and generate biodiversity in the CFR. We
discuss the difficulty of assessing the requirements for pattern versus pro
cess representation in the face of ongoing threats to biodiversity, the dif
ficulty of testing the predictions of alternative conservation systems, and
the widespread need in conservation planning to incorporate and set target
s for the spatial components (or surrogates) of processes.