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Secondary metabolites (SMs) are organic molecules that have a wide range of chemical structures and biological functions. SMs, especially flavonoid, have been recently suggested in playing important roles as antioxidants. They appear to be induced by a variety of environmental factors including fungal elicitors, light, ultraviolet radiation, interactions with microorganisms, wounding, metal stress, temperature changes, drought and nutrient depletion. These molecules are commonly synthesized in different parts of the plant (cells, leaves, stem, roots, vacuole of plant cells) and protect the plant against adverse conditions, such as microbial and herbivore attacks. Some SMs had a significant impact on human health as they are important components of the daily diet and may help prevent human diseases. The structural and regulatory genes play important roles in the biosynthesis of secondary metabolites. In this chapter, recent research developments on the structural genes and regulatory genes that are involved in the biosynthesis of SMs and plant developments are discussed, focusing on the flavonoid biosynthesis pathway.