The relict, endemic taxa Allopaa and Chrysopaa are key elements of the Hindu Kush-Himalayan amphibian fauna and potentially share a similar biogeographic evolution, making them important proxies for the reconstruction of the palaeoenvironmental and palaeotopographic history of the Himalaya-Tibet-Orogen. However, little is known about the taxonomy, phylogeography, genetic diversity and distribution of these taxa. We here provide new molecular data on Himalayan spiny frogs and species distribution models (SDMs) for A. hazarensis and C. sternosignata. The results reveal a better resolved phylogeny of these frogs compared to previous trees and strongly support the placement of A. hazarensis in the genus Nanorana. We further identify a so far unknown clade from the western Himalayas in Nanorana, apart from the subgroups Chaparana, Paa and the nominal Nanorana. In A. hazarensis, genetic diversity is relatively low. The results strengthen support for the recently proposed out-of-Tibet-into-the-Himalayan-exile hypothesis and a trans-Tibet dispersal of ancestral spiny frogs during the Palaeogene. Moreover, SDMs provide the first detailed distribution maps of A. hazarensis and C. sternosignata and strong evidence for distinct niche divergence among the two taxa. Our findings contribute to the knowledge about the distribution of these species and provide basic information for guiding future conservation management of them.