The Sierra de La Laguna, in the southern part of the state of Baja California Sur, Mexico, was decreed a biosphere reserve in 1994. It harbors relict plant communities with a high level of endemism. Floristic research has established that the two main communities, the oak–pine woodland (OPW) and the dry tropical forest (TDF), harbor 43 and 33 endemic species, respectively. We segregate the reserve surface into seven major habitats and each endemic species were assigned a hierarchic value into an abundance-distribution scale, useful as dominance ranking. Using such scale, we found that almost half of the species are in the lowest rank (low abundance and aggregate distribution). Using GIS, we obtain the surface for each habitat, where mountainsides represent the largest in the reserve area. We obtained an index of importance from the proportion of endemic species by habitat and its surface occupied, founding that, in spite of the small and fragmented nature of the upland riparian habitats, they have the greatest index value. Consequently, for future conservation plans in the reserve, these habitats should be considered remarkable sites, meriting better attention to ensure endemic plant preservation. Also, since 86% of the endemic species appear in one, two or three habitats, a high dependency on particular environmental conditions is suggested for them.