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Environmental stress at high altitudes drives the development of distinct adaptive mechanisms in plants. However, studies exploring the genetic adaptive mechanisms of high-altitude plant species are scarce. In the present study, we explored the high-altitude adaptive mechanisms of plants in the Himalayas through whole-genome resequencing. We studied two widespread members of the Himalayan endemic alpine genus <i>Roscoea</i> (Zingiberaceae): <i>R. alpina</i> (a selfing species) and <i>R. purpurea</i> (an outcrossing species). These species are distributed widely in the Himalayas with distinct non-overlapping altitude distributions; <i>R. alpina</i> is distributed at higher elevations, and <i>R. purpurea</i> occurs at lower elevations. Compared to <i>R. purpurea</i>, <i>R. alpina</i> exhibited higher levels of linkage disequilibrium, Tajima’s <i>D</i>, and inbreeding coefficient, as well as lower recombination rates and genetic diversity. Approximately 96.3% of the genes in the reference genome underwent significant genetic divergence (<i>F</i>_ST ≥ 0.25). We reported 58 completely divergent genes (<i>F</i>_ST = 1), of which only 17 genes were annotated with specific functions. The functions of these genes were primarily related to adapting to the specific characteristics of high-altitude environments. Our findings provide novel insights into how evolutionary innovations promote the adaptation of mountain alpine species to high altitudes and harsh habitats.