We evaluated the effectiveness of protected areas in the Baja California Peninsula for the conservation of endemic species of reptiles, birds, and mammals by using a combination of approaches. We built a collection database consisting of 7912 unique specimens from 826 sites. We found 42 endemic species on the peninsula: 17 microendemics, 13 mesoendemics, and 12 macroendemics. Our findings show that 37 endemic species (88% of the total endemics) are found within the boundaries of these eight protected areas, and five microendemics are gap species (unrepresented). Complementarity values show a low level of diversity between the endemic vertebrate faunas of the adjacent areas, Valle los Cirios and Vizcaino (ICC = 0.44). A much higher complementarity (ICC = 0.86) was found in the Valle los Cirios and La Laguna areas, more than 400 km apart. The National Park Constitucion de 1857 has no terrestrial endemic vertebrates within its boundaries. About 60% of the peninsular endemic vertebrates are included in the Mexican list of species at risk. We identified areas of high concentration of terrestrial-endemic vertebrate species in the Baja California Peninsula: one in the north in the San Telmo-San Quintin region, a second in Planicies de Magdalena, and a third in Sierra La Giganta in the middle south, and a region in Sierra La Laguna in the southern part of the peninsula. Our results provide a robust diagnosis of the effectiveness of the protected areas for the conservation of endemic vertebrates that can be useful for further studies and for improving the protection of these regional biodiversity elements.