Proanthocyanidins and anthocyanins derived from the phenylpropanoid pathway most likely play a protective function from pathogens and UV light exposure within the plant and, in addition, act as signal molecules in plant-microbe interactions. The metabolites are now attracting attention because of the medicinal and nutritional values due to their antioxidant properties and flavors. Three independent loci (I, R, and T) control pigmentation of the seed coats determined by proanthocyanidins and anthocyanins in soybean (Glycine max). The I locus controls distribution of anthocyanin and proanthocyanidin pigments, which in its dominant form exhibits homology-dependent gene silencing leading to a yellowish seed coat. The R and T genes determine the anthocyanin and proanthocyanidin products and specific seed coat color such as black, imperfect black, brown, or buff. The I and T loci have been cloned. The objectives of this study were to develop PCR-based molecular markers cosegregating with the genetic loci controlling the biosynthesis of these interesting metabolites using public soybean EST and genomic sequence data. Thus far, we have developed SSR, SNP, and STS markers cosegregating with the I, R and T loci. Work is in progress to develop markers cosegregating with other genetic loci. The markers will facilitate markers-assisted selection of seed coat colors in molecular breeding programs.