Sky Islands are high-elevation environments that are separated by warmer, low elevations, forming natural patches of unique montane habitat that often persist through changing climates. Peninsular India was ancestrally forested and has gradually become more arid since at least the Oligocene, and open landscapes have dominated since the middle-late Miocene. Mesic forests today are largely restricted to coastal mountains and some other montane habitats. A mitochondrial phylogeny and fossil-calibrated timetree of Indian Hemiphyllodactylus reveal an Indochinese origin and an endemic radiation with 12 species-level lineages, where a single species was known, that diversified in the Oligocene-Miocene across montane forest habitats in the Eastern Ghats and south India. The phylogeny also suggests the discontinuous Eastern Ghats mountain range encompasses two distinct biogeographic entities: north and south of the Pennar/Krishna-Godavari River basins. This study highlights the deep history of the region and the importance of montane habitats as islands of unique biodiversity that have persisted through millions of years of changing climates. We describe three new species: Hemiphyllodactylus arakuensis sp. nov., H. jnana sp. nov. and H. kolliensis sp. nov. from montane habitats above 1000 m. The montane habitats of these species are emerging hotspots of reptile endemism, and this study emphasizes the need for systematic biodiversity inventory across India to uncover basic patterns of diversity and distribution.