Grape flavonoids, especially anthocyanins, are important contributors to color, taste, antioxidant and nutraceutical properties - such as protection against cardiovascular diseases and cancer - for fresh fruit and processed products. Breeding programs and wild Vitis germplasm banks include a wide genetic variation in anthocyanin biosynthesis, and metabolism-associated traits, indicating a complex genetic control of the process throughout plant development. Expressed sequence tag (EST) and genomic databases were investigated using bioinformatic tools to identify SNP markers present in structural and regulatory genes associated with anthocyanin metabolism in Vitis. We have identified more than 1,000 putative SNPs in nine structural and twelve regulatory genes of the anthocyanin metabolism in Vitis. The data suggest that the identified genetic variation is sufficient to distinguish among V. vinifera cultivars, hybrids and wild species. Regulatory genes were shown to be more rapidly evolving than structural enzyme-coding sequences. The evolutionary rate of the sequences associated with regulatory factors also appear to be differential, with higher levels of conservation found in the MYB family of transcriptional regulators associated with anthocyanin regulation. After experimental validation, the predicted polymorphisms will provide tools for further mapping, genome structure and functional studies.