Lizards of the genus Dendragama are endemic to the highland cloud forests of Sumatra’s Barisan Mountain Range in western Indonesia, and recent studies have uncovered widespread diversity within the genus. Here, a suite of morphological characters and mitochondrial DNA are used to compare three geographically isolated populations of D. boulengeri from (1) Mount Kerinci in Jambi province, (2) Mount Marapi of west Sumatra, and (3) the Karo Highlands of north Sumatra. Additional phylogeographic analyses with two recently described sister species, D. australis and D. dioidema were conducted. Five genetically distinct clades of Dendragama, all distributed allopatrically of one another were identified and some are suspected to inhabit small distributions. Morphological and genetic data confirm the Karo Highlands population D. schneideri (previously Acanthosaura schneideri Ahl, 1926) should be revalidated from the synonymy of D. boulengeri. Dendragama schneideri is endemic to montane forests of the Karo Highlands surrounding Lake Toba in Sumatra Utara province. Pairwise genetic distances of 6–11% separate D. schneideri from congeners. Two distinct clades of D. boulengeri from Mount Kerinci and Mount Marapi were identified, which are 5.0% genetically distant from one another. Using morphological characters, we provide the first key for distinguishing between species of Dendragama. Based on biogeographic patterns and levels of genetic variation it is suspected that at least 18 other isolated cloud forest locations may hold new species or divergent populations of Dendragama but lack survey work. Collectively, these comparisons among populations of montane lizards further elucidate the complex biogeographic history of Sumatra’s montane forest species and the first phylogeny of the genus Dendragama.