Different physiognomies at Parque Nacional da Serra das Confusões (PNSCo) were intensively sampled aiming to access the distribution pattern of its herpetofauna. Sixty six species were found in the park (47 reptiles and 19 amphibians); the rarefaction curve for lizards, although not fully stabilized in an asymptote, indicates that the sampling effort was enough to reveal most lizard species occurring in the area; and richness estimators recovered values close to observed. For amphibians, the curve shows a weak tendency to stabilization with richness estimators indicating that additional records could be done. Field work carried out at PNSCo has highlighted an unique herpetofauna: five new species were described and there are three candidates as new species. The regional list including Cerrados's units - Estação Ecológica Serra Geral do Tocantins (EESGT) and Estação Ecológica de Uruçuí-Una (EEUU) with Caatinga's ones - PNSCo and Parque Nacional da Serra da Capivara (PNSCa), shows a high herpetofaunal diversity (191 species) to the region. The cluster analysis recovered the Cerrados's units and Caatinga's ones, in separate clusters evidencing a species turnover between domains, despite its geographical proximity. Thus, although there is widespread fauna throughout region shared by the units, each reserve holds its own faunal identity, harboring a singular assemblage of species.