Alpine medicinal plants underpin mountain ethnopharmacopoeias and provide model systems for studying adaptation to extreme environments. This chapter synthesizes current advances in molecular phylogeny and phylogeography of alpine medicinal plants, with an emphasis on widely used markers (nuclear internal transcribed spacer, chloroplast regions, complete plastid genomes), next-generation sequencing approaches (restriction-site associated DNA sequencing, genome skimming), and integrative analyses that couple genetic variation with ecological and biogeographic data. Using representative taxa—including Rhodiola (Crassulaceae), Saussurea and Artemisia (Asteraceae), and Gentiana (Gentianaceae)—we highlight patterns of rapid diversification, glacial refugia, postglacial range dynamics, and phylogenetic–taxonomic resolutions relevant to conservation and sustainable use. We also outline a transparent workflow from field sampling and laboratory pipelines to computational inference (maximum likelihood, Bayesian frameworks) and phylogeographic modeling (coalescent analysis, haplotype networks, species distribution modeling). The synthesis frames alpine diversity in a comparative context across the Himalayas, the European Alps, the Andes, and the Tibetan Plateau, setting the stage for multi-omics and conservation genomics in later sections. Findings inform taxonomy, prioritization of evolutionarily significant units, and climate-resilient management strategies.