The Coastal Forests of Eastern Africa (CFEA) are a global biodiversity hotspot, consisting of a complex landscape of savannah and fragmented forest patches heavily influenced by late Pleistocene climate cycles and sea level changes. Although most habitats have contracted and expanded with the changing conditions, it has been predicted that some remained constant since the last interglacial period (120kya) allowing the persistence of lineages that became locally extinct in the surrounding landscape. To date, explanations of diversity and endemism in the CFEA have been based on knowledge of taxonomically recognised species ranges, failing to include phylogenetic information. We address these shortcomings by investigating endemism across the whole amphibian assemblage (species level and below), integrating spatial and newly generated phylogenetic data from across the coastal forests in Tanzania and Kenya. Our results show that endemism is concentrated in five major areas; three areas of coastal dry forest and two areas of transitional rainforest on the lower slopes of the nearby Eastern Afromontane region. These areas correspond to predicted habitat stability, likely playing a major role in the maintenence of biodiversity in this region, and should be considered as important evolutionary refugia.