Medicinal plants are a vital source of new bioactive compounds due to their ecological biodiversity and varied chemical properties of each species. Phenotypic selection coupled with the evaluation of genotypes based on the chemical profile can be used for the development of a high-yielding variety. However, most of the raw material that has been used for commercial production of herbal products is mainly derived from wild sources, with little knowledge of the quality of genetic materials. Thus, three medicinal species, Chromolaena odorata (Siam weed), Andrographis paniculata (Creat), and Baeckea frutescens (False ru), were chosen based on their significant benefits to human health. These medicinal species have been traditionally used to treat various illnesses, and have been shown to possess anti-inflammatory, antimicrobial, anticancer, and antioxidant properties. This paper highlights the harvesting method and collection of accessions from natural habitats for the selection of superior genotypes. Individual plants having superior phenotypic characteristics and bioactive compounds were identified. We successfully developed appropriate propagation techniques for each species for the mass production of high-yielding planting material. The establishment of breeding activities for these medicinal plants will provide quality raw materials to support the herbal industry in increasing the value of pharmaceutical products. These efforts will also ensure the sustainable production of high-quality planting materials for the establishment of herbal plantations.