Information gaps about species distribution hamper the evaluation of conservation status and decisions on biodiversity conservation, affecting to a greater extent, areas with high species richness and endemism. In this context, biological inventories are an important tool to fill these gaps by providing data on the composition, richness, and abundance of species in each locality. The Parque Nacional da Serra das Lontras (PNSL) protects various mountain range just up 1000 m. in altitude, and, together with other conservation units, forms an ecological corridor in the southern part of the state of Bahia, within the Atlantic Forest hotspot. We conducted systematic samplings on transects, and opportunistic records in ponds and streams, in order to record amphibian and reptile species in the PNSL. We complement the sampling with the information available in the literature and in scientific collections. A total of 100 species (49 amphibians and 51 reptiles) was recorded, 53 of them endemic to the Atlantic Forest, 13 to the state of Bahia, and two known only from the PNSL. Hylidae was the most diverse family of amphibians (22 spp.) and Colubridae of reptiles (33 spp.). New information on the distribution and natural history of these species is provided, many of which have not yet been assessed by the IUCN while others have already been categorized as at risk of extinction at the regional level. Results confirm the high species richness and rates of endemism in southern Bahia and highlight the importance of protecting high altitude areas for the preservation of evolutionary and ecological processes within the Atlantic Forest.