Effective conservation of rare plant species requires a detailed understanding of their unique distributions and habitat requirements to identify conservation targets. Research suggests that local conservation efforts may be one of the best means for accomplishing this task. We conducted a geographical analysis of the local distributions of rare plants in Napa County, California, to identify spatial relationships with individual habitat types. We measured the potential contribution of individual habitats to rare plant conservation by integrating analyses on overall diversity, species per area, specificity-weighted richness, presence of hotspots, and the composition of the rare plant community in each habitat type. This combination of analyses allowed us to determine which habitats are most significant for rare plant conservation at a local scale. Our analyses indicated that several habitat types were consistently associated with rare plant species. In broad terms, grasslands, oak forests, coniferous forests, wetlands, serpentines, chaparral, and rock outcrops were most consistently highlighted. No single habitat stood out in every analysis however, and therefore we conclude that careful selection of an assemblage of habitats that best represents diverse, restricted and unique rare plant communities will be the most efficient approach to protecting rare plant habitat at local scales. Accordingly we present a means of identifying conservation targets and protecting global biodiversity through local efforts.