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Species extinction rates 100 to 1000 pre-human levels are threatening the planet’s biodiversity. The Amazon rainforests are of particular importance to protecting species because of their extremely high levels of biodiversity. Faced with losses from deforestation of 20 % in the last 40 years and expecting to lose another 20 % in the next 20 years, governments and conservationist organizations must begin planning in order to mitigate species extinctions and the destruction of ecosystems. This master’s project creates a GIS-based planning tool for conservation practitioners that locates and prioritizes new protected areas in the Madre de Dios watershed in southeastern Peru. The tool is based on distributions of bird and mammal species endemic to Peru and Bolivia, ecological systems, and development threats. This study (1) locates centers of high endemic species richness (2) locates centers of high endemic species richness for threatened species falling in the IUCN Red List categories of Critically Endangered, Endangered, and Vulnerable (3) and models conservation values based on (1) and (2) to identify and locate centers of conservation value, This study als