Flavonoid-derived plant natural products have long been known to function as floral pigments for the attraction of insect pollinators, as signal molecules for beneficial microorganisms in the rhizosphere, and as antimicrobial defense compounds. New functions for flavonoid compounds continue to be found, particularly in plant-microorganism signaling, and there has been an explosion of interest in flavonoids and isoflavonoids as health-promoting components of the human diet. The flavonoid and isoflavonoid pathways are probably the best characterized natural product pathway in plants, and are therefore excellent targets for metabolic engineering. Manipulation of flavonoid biosynthesis can be approached via several strategies, including sense or antisense manipulation of pathway genes, modification of the expression of regulatory genes, or generation of novel enzymatic specificities by ra-tional approaches based on emerging protein structure data. In addition, activation tagging provides a novel approach for the discovery of uncharacterized structural and regulatory genes of flavonoid biosynthesis.