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The Peninsula of Baja California, Mexico has long been recognized as a hotspot for plant richness and endemism. However, its extraordinary diversity is not adequately protected by the existing protected areas. We analyzed the distribution of the endemic vascular flora of the peninsula, and its presence or absence in protected areas. We also identified regions with greater numbers of endemic species not currently under protected status. The families Asteraceae, Cactaceae, and Fabaceae alone contain 40% of the endemic species. All the peninsular species within the Begoniaceae, Thymeliaceae, Araliaceae and Hippocastanaceae are endemic. Of the total number of endemic taxa in the region, 76.4% are present within protected areas. The endemic genera Adenothamnus, Carterothamnus, Faxonia, and Ornithostaphylos are entirely absent from protected areas. Of the 567 endemics found in protected areas 75 represent varieties or subspecies Of the 175 not found in protected areas 21 are varieties or subspecies. A gap analysis identified that the areas with the highest number of unprotected endemic species are in the Mediterranean-type ecosystems of the north-west part of the peninsula and in the deciduous dry tropical communities of the cape region at the southernmost tip of Baja California. Our findings suggest that it is necessary to create several protected areas along the peninsula for the successful conservation of rare and endemic taxa These new areas should encompass a latitudinal gradient of biogeographical units (including Mediterranean communities and montane habitats of the Sierras) along the peninsula. Inglés