Conservation planning has tended to focus more on pattern (representation) than process (persistence) and, for the former, has emphasized species and ecosystem or community diversity over genetic diversity. Here I consider how best to incorporate knowledge of evolutionary processes and the distribution of genetic diversity into conservation planning and priority setting for populations within species and for biogeographic areas within regions. Separation of genetic diversity into two dimensions, one concerned with adaptive variation and the other with neutral divergence caused by isolation, highlights different evolutionary processes and suggests alternative strategies for conservation. Planning for both species and areas should emphasize protection of historically isolated lineages (Evolutionarily Significant Units) because these cannot be recovered. By contrast, adaptive features may best be protected by maintaining the context for selection, heterogeneous landscapes, and viable populations, rather than protecting specific phenotypes. A useful strategy may be to (1) identify areas that are important to represent species and (vicariant) genetic diversity and (2) maximize within these areas the protection of contiguous environmental gradients across which selection and migration can interact to maintain population viability and (adaptive) genetic diversity. These concepts are illustrated with recent results from analysis of a rainforest fauna from northeast Australia.