Plant genetic diversity underpins the biosynthesis of a vast array of bioactive compounds that play essential roles in ecological adaptation, human health, and drug discovery. Secondary metabolites such as alkaloids, terpenoids, flavonoids, and phenolics are highly diverse, shaped by both genetic and environmental factors, and often occur in specific cultivars, populations, or species. Advances in evolutionary theory, genomics, and pan-genomics have revealed that processes including gene duplication, whole-genome duplication, horizontal gene transfer, and epigenetic regulation drive chemical diversification and the emergence of novel metabolites. Biosynthetic gene clusters and transcriptional regulators further coordinate specialized metabolism, reflecting a complex interplay between genome architecture and ecological selection pressures. Case studies from Centella asiatica, Panax ginseng, Panax vietnamensis, and Thymus vulgaris highlight the close association between genetic variation and chemical phenotypes, demonstrating how genetic diversity determines chemotype formation, metabolite profiles, and therapeutic potential. These insights emphasize biodiversity as an invaluable resource for developing novel pharmaceuticals, nutraceuticals, and value-added products while underscoring the urgent need for conservation and sustainable use of plant genetic resources in the face of global biodiversity loss.