Natural Protected Areas (NPAs) includes important species richness, and it is assumed that these are the best areas for biodiversity conservation. There are certain doubts, however, about the effectiveness of the NPAs in developing countries, where economic resources for conservation are scarce and NPAs are not monitored and managed efficiently. In the present study we assessed the species richness, diversity, abundance, and functional guilds of amphibians and reptiles inside and outside of the NPA Reserva Estatal de la Biósfera Sierra San Juan (REBSSJ), Nayarit, Mexico. Our results showed that species numbers of amphibian and reptiles were higher outside than inside the reserve, as well the individual number distributed among species, except for lizard species. Analyses of functional guilds showed that both richness and functional dispersion were greater in amphibians and reptiles outside the reserve. Likewise, outside the reserve we recorded a higher species number with some category of risk at the national level (NOM-059), international level (IUCN), and also by using the Environmental Vulnerability Score (EVS) algorithm. The results suggest that areas outside of the reserve are crucial to the maintenance of regional biodiversity, due to high complementarity with species composition inside of the reserves. These data can be used to implement conservation measures that include a new demarcation of the reserve and the consideration of surrounding areas to include a great number of species.