Garnacha Tintorera (also known as Alicante Bouschet) is one of the few V. vinifera grape cultivars with red-colored berry flesh. The study of the phenolic composition of both berry flesh and skin of Garnacha Tintorera grapes shows interesting findings. Anthocyanins were asymmetrically distributed within grape flesh and skins. Malvidin derivatives dominated in skin, followed by peonidin-type anthocyanins; in contrast, the flesh almost exclusively contained peonidin 3-glucoside. In addition, LC-UV-vis and LC-MS evidence suggest the presence of small amounts of peonidin 3,5-diglucoside and a second peonidin dihexoside derivative, and, very likely, the first report of the occurrence of pelargonidin 3-glucoside and its acetyl and p-coumaroyl derivatives in V. vinifera grapes. Flavonols also occurred in the flesh of Garnacha Tintorera grapes, but its flavonol profile showed lower contribution of trisubstituted flavonoid structures (myricetin, laricitrin, and syringetin) when compared to that of skin. The skin of Garnacha Tintorera grapes contained hydroxycinnamic acids in higher amounts than in flesh, caftaric acid being the main derivative found, and coutaric acid accounting for its highest proportion in the skin. The phenolic composition of the whole grape berries reflected the average of the differences described for the two aforementioned berry parts, and subsequently, the red wines made from these grapes had a phenolic composition closer to that shown by the whole berries. The formation of anthocyanin-derived pigments in Garnacha Tintorera red wines makes necessary the use of LC-MS for detecting the minor pelargonidin-based anthocyanins and peonidin dihexoside, which could be suggested as chemical markers for cultivar authentication of this grape cultivar and its wines.