The color that results from anthocyanin accumulation has a direct effect on the dietary and market values of fresh fruit. Fruit color pigments such as anthocyanins are produced via the flavonoid pathway, where the biosynthetic genes are coordinatedly regulated by the myeloblastosis, basic helix–loop–helix, and WD40 a beta-transducin repeat, which is a short structural motif consisting of about 40 amino acids that commonly terminating in a tryptophan–aspartic acid (W–D) dipeptide “MYB-bHLH-WD40/WDR” (MBW) regulatory complex. This article discusses the representatives of this regulatory complex, such as bHLH, MYB, WD40, and their regulatory role in fruit coloration. Further, the joint role of MYBs, bHLH TFs, and structural genes has been described in this article. This article will help plant breeders in the future to breed colorful, anthocyanin, and nutrient-rich fruit-bearing plant species.