Information on the composition of amphibian and reptile communities in localities of the Santa Fe National Park (PNSF) and the General of Division Omar Torrijos Herrera National Park (PNSF) is presented. Both protected areas were impacted respectively in 2002 and 2004 by chytridiomycosis, a disease exclusive to amphibians and caused by the fungi Batrachochytrium dendrobatidis. Transect sampling using the technique of visual encounter survey during day and night were used. In february 2013 in the PNSF and september 2012 in the PNGDOTH. In the PNSF I recorded 56 amphibians of 12 species and 43 reptiles of 11 species. In the PNGDOTH 91 amphibians of 19 species and 42 reptiles of 17 species. According to the sampling, the diversity of amphibians in both localities, measured through ecological indexes, is moderately high and without dominance of a species. The arrangement of reptiles in the locality of the PNSF has a lower diversity and with dominance of a pair of species in comparison to the arrangement in the locality of PNGDOTH. A standardized sampling effort is needed at both locations for increase comparative certainty. In this work are registered many species valuable for conservation in Central America and stand out in order to improve the management of both protected areas.