In an era of rapid climate change, it is important to understand how naturally rare species—such as those with small geographic ranges, specialized habitat requirements, and low local abundances—have persisted in time and space. In the flora we studied, species with all three forms of rarity inhabited geographic regions with more benign climates (higher total and summer rainfall, less extreme seasonal temperatures) and larger areas of their specialized habitat within 10 km than did more common species in the same habitats. Similar differences were also seen in congener-only comparisons. We found no evidence for two nonexclusive alternatives, that naturally rare species had more extinction-resistant life history traits, or that they belonged to more rapidly speciating taxa than common species. Understanding the association of rare species with benign environments may help in the design of effective conservation strategies for geographic regions of high diversity and endemism under changing climates. In particular, our findings highlight the extra climatic sensitivities of rare species with edaphic or other specialization, and how the needs of these species may be met by either refugia or translocation strategies.