Question Can we recognize areas of high endemism and high endemic richness, using data from collections, and what are the ecological variables that best explain these areas?Location: Peninsula of Baja California, Mexico.Methods: We analysed the distribution of 723 endemic vascular plants species along the peninsula of Baja California and neighbouring islands distributed in 218 cartographic cells 15′ × 20′ in size. By means of a residual analysis, we identified areas of significantly high endemic species richness, and we calculated the degree of endemicity (or rarity) in each cell by giving to each species a weight factor inversely proportional to the land area it covers.Results: Nine regions of high-endemicity and/or high endemic species richness were found.Discussion and conclusions: The analyses of rarity and endemic species richness showed two contrasting scenarios: High endemicity values in oceanic and sky islands accounts for a high number of species with a restricted distribution, promoted most likely by genetic isolation and high environmental heterogeneity. High endemic richness along the peninsular coast is related to ecotonal transition along vegetation types. After correcting for collection effort (i.e. the number of specimens collected within a cell), we found the phytogeographic region and altitudinal heterogeneity to be the variables that best predicted endemic richness. Both high endemism and high endemic richness have distinct geographic patterns within our study region. The nine endemic regions provide elements for priority definitions in future conservation programs.