Medicinal plants have long been utilized in traditional medicine and worldwide ethnomedicine. This chapter presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of plant genotype and metabolic phenotype, interaction between medicinal plant genomes and environment, and correlation between genomic diversity and metabolite diversity, etc. The uses of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants to expedite the medicinal plant breeding and transform them to the living factory of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural product-based drug discovery and development. The representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.