Tibetan frogs, Nanorana parkeri, are differentiated genetically butnot morphologically along geographical and elevational gradientsin a challenging environment, presenting a unique opportunity toinvestigate processes leading to speciation. Analyses of whole ge-nomes of 63 frogs reveal population structuring and historical de-mography, characterized by highly restricted gene flow in anarrow geographic zone lying between matrilines West (W) andEast (E). A population found only along a single tributary of theYalu Zangbu River has the mitogenome only of E, whereas nucleargenes of W comprise 89–95% of the nuclear genome. Selectionaccounts for 579 broadly scattered, highly divergent regions(HDRs) of the genome, which involve 365 genes. These genes fallinto 51 gene ontology (GO) functional classes, 14 of which arelikely to be important in driving reproductive isolation. GO enrich-ment analyses of E reveal many overrepresented functional cate-gories associated with adaptation to high elevations, includingblood circulation, response to hypoxia, and UV radiation. Fourgenes, including DNAJC8 in the brain, TNNC1 and ADORA1 in theheart, and LAMB3 in the lung, differ in levels of expression be-tween low- and high-elevation populations. High-altitude adapta-tion plays an important role in maintaining and driving continuingdivergence and reproductive isolation. Use of total genomes en-abled recognition of selection and adaptation in and betweenpopulations, as well as documentation of evolution along a step-ped cline toward speciation.