The current study attempts to explore the diversity patterns and the ecological structure of herpetofauna in order to provide a guideline for its conservation management, taking as case study the Dadia national park, in Greece. We surveyed 36 sites by conducting time constraint visits and random transects to sample semi-aquatic (amphibians and freshwater terrapins) and terrestrial (lizards and terrestrial tortoises) herpetofauna respectively. We recorded 20 herpetofauna taxa, including five protected species. The park authorities should maintain brooks as a high priority habitat for semi-aquatic herpetofauna, periodically flooded land and lowland streams as important habitats, and to a lesser degree anthropogenic wet habitats. Semi-aquatic species have narrow habitat requirements related to substrate type and humidity. Terrestrial herpetofauna species are influenced by the degree of shade and the type of substrate; they favour a diversity of semi-open habitats (open oakwoods, heaths), located in the buffer zone rather than in the core of the park that contains densely forested habitats. Management focusing on raptors, the initial conservation priority of the national park, is compatible with the conservation of the terrestrial herpetofauna, as the proposed maintenance of an open forest structure is beneficial for terrestrial herpetofauna as well. Our research indicates that future management programs will have to address the needs of herpetofauna species independently and that they should also be integrated in the monitoring programme of the park, with emphasis on the conservation status and trend of the five protected species.