Pigmentation by flavonoid pigments is the oldest trait employed for studies in genetics. In the current chapter, we describe application of the flavonoid biosynthesis (FB) genes as a model in the study of regulatory-target gene relationships in allopolyploid wheat genome (Triticum aestivum, AABBDD, 2n = 6x = 42) and gene functioning in a foreign background in wheat-alien hybrids. Investigation of this multicomponent gene system showed that FB gene regulation cuts across genomes of allopolyploid wheat, the regulatory FB genes contribute more to the functional divergence between the diploid genomes of allopolyploid wheat than do the structural genes, and a good cooperation of the wheat and alien FB gene systems is observed in wheat-alien hybrids.