Jackson's Forest Lizard (Adolfus jacksoni) is widespread throughout the highlands of the Albertine Rift, southern Uganda, western and central Kenya, and northern Tanzania. To understand the population genetics and phylogenetic relationships of this widespread taxon, we sequenced two mitochondrial (16S and cyt b) and two nuclear (c-mos and RAG1) genes from multiple populations. Population genetics analyses suggested a high degree of genetic differentiation among A. jacksoni populations, reflecting the high-elevation montane “islands” that they inhabit. Populations connected by a network of mountain ranges generally showed lower levels of genetic partitioning than those isolated by low-elevation habitat. Results from phylogenetic analyses and additional morphological data indicated that Adolfus jacksoni occurs throughout the Albertine Rift, likely from the Kabobo Plateau to the Lendu Plateau of Democratic Republic of the Congo, as well as southern Uganda, Mt. Elgon, and the highlands of western Kenya on the western side of the Kenyan Rift. Adolfus kibonotensis is removed from the synonymy of the latter taxon, elevated to full species, and recognized from the central Kenyan highlands to northern Tanzania on the eastern side of the Kenyan Rift. A new Adolfus species is described from the Mathews Range in central Kenya.