Flavonoid compounds are secondary metabolites widely accumulated in vascular plants and to a lesser extent in mosses. They accumulate in all organs and tissues, at different stages of development, and depending on the environmental conditions. Beside their multiple roles in plant development and adaptation to the environment, these molecules are of major interest for human nutrition and health. Indeed, they contribute to the organoleptic quality of plant-derived products (colour, taste, flavour, etc.), and, in addition, they have been shown to be beneficial to human health and in prevention of cell ageing. Flavonoids play a central role in fruit colour, flavour and health attributes, in addition to plant defense against various stresses. Flavonoids appear to regulate the expression of many genes. Although flavonoid biosynthesis has received much attention concerning the structural genes and expression of the associated transcription factors (TFs), but unfortunately little information is available regarding the proportion of contribution of various structural elements. Also, we have very limited information on their molecular mechanisms of action, morphological, physiological and phenotypic of plant is always affected by flavonoids regulation in plants assisted with flavonoids associated genes regulations. Two factors of concerns are the type and the endogenous concentration of flavonoids which play key roles in the degree of plant phenotype and stress defending.