The montane agamid lizard Japalura austeniana (Annandale, 1908), is rare and is distributed across parts of the eastern Himalayas of India and China. Support from molecular and morphological data provides evidence for the existence of a species complex in the populations referred to that binomen, and we here describe a morphologically cryptic allied new species. Evidence from molecular data suggests the presence of additional undescribed species across the distribution of that species complex. Elevation might be the restricting factor for gene flow explaining most of the diversification of that montane species complex across the Himalayas.