The high loss rate of forest ecosystem by deforestation in the Trans-Mexican Volcanic Belt is one of the principal ecological problems of central Mexico, even in natural protected areas. We compiled a checklist and determined β-diversity indexes of amphibians and reptiles of the highly disturbed protected area, La Malinche National Park (LMNP) in Mexico, to determine the principal habitats for herpetofaunal conservation. After our extensive eight-year field sampling, we documented 28 species (nine amphibians and 19 reptiles), representing 11 families and 18 genera; four of these species are new records for LMNP. Of the species, 89% are endemic to Mexico. The IUCN Red List considers 22 species as Least Concern, one as Near Threatened, and four as Vulnerable. Meanwhile, the Environmental Viability Scores categorize three species as low vulnerability, 15 as medium, and 10 as high. According to the Mexican list of protected species, eight species are under Special Protection and nine are considered Vulnerable. The dissimilarity index between habitat types (βsør) in both groups is high, principally due to the environmental gradient generated by the altitudinal range.Abiesand Pine forest are high diversity areas for amphibians and reptiles, respectively, and must be considered for special protection. LMNP hosts more than 60% of the herpetofauna of Tlaxcala and is the principal “conservation island” for this state. Therefore, based on the percentage of state species represented, endemism and the current social and ecological problems, additional efforts that involve the local communities to protect the biodiversity of this National Park are necessary.
