In the last decade, great progress has been made in clarifying the main determinants of anthocyanin and flavonol accumulation in grape berry skin. However, the molecular details of the fine variation in anthocyanin and flavonol content and composition at harvest among cultivars, which contributes to wine typicity, are still not completely understood. To shed light on this issue and on the metabolic interdependency in the synthesis of the two flavonoid classes, we adopted an integrative approach combining metabolic, genetic and transcriptional sources of information based on a 170 F1 progeny from ‘Syrah’ x ‘Pinot Noir’ cross. New candidates involved in the genetic control of anthocyanin biosynthesis were identified by exploring the gene predictions in 17 mQTL regions and their expression profile during ripening in individuals with contrasting anthocyanin accumulation. New information on some aspects scarcely investigated so far, like anthocyanin sequestration (genes encoding for GST and MATE proteins) and degradation (genes encoding for peroxidases, laccases, and polyphenol oxidases), or completely neglected such as acylation (genes encoding for BAHD and serine carboxypeptidase-like families) was acquired. Interestingly, the analysis of the flavonol genetic control led to the discovery of a large effect QTL, co-localizing with the major locus controlling the anthocyanin content. On the other hand, flavonol-specific mQTL regions contained genes encoding for MYB and bZIP transcription factors, methyltranferases and glucosyltranferases, proteins belonging to UV-B signalling pathway, which seems not to be associated to anthocyanin metabolism.