This study focuses on amphibian species diversity in the lowland Amazonian rainforest of southern Peru, and on the importance of protected and non-protected areas for maintaining amphibian assemblages in this region. We compared species lists from nine sites in the Madre de Dios region, five of which are in nationally recognized protected areas and four are outside the country's protected area system. Los Amigos, occurring outside the protected area system, is the most species-rich locality included in our comparison. Overall, species similarity is relatively high among various localities in Madre de Dios. Among the 114 species recorded in Madre de Dios, nine (7.9%) have only been recorded on land outside of protected areas. This number emphasizes the need to conserve additional sites in the region, especially in the face of rapid habitat destruction. In addition, preliminary results from comparisons of species richness and abundance at the Los Amigos site suggest that forest type may affect the species composition, abundance, and distribution of amphibians at the local scale (area < 1000 ha). These results have wider implications for reserve design and habitat conservation decisions. We also present data on the conservation status of the amphibians of Madre de Dios according to IUCN and CITES categories. © 2009. Rudolf von May. All Rights Reserved.