Wild grapevine (Vitis vinifera L., subsp. sylvestris) was found recently along the rivers in the karst landscape of the eastern Adriatic region, which includes Croatia and Bosnia and Herzegovina. The wild grapevine is almost extinct and grows in a restricted habitat in Europe. The anthocyanin profile of red grape berries from naturally growing populations of female wild var. sylvestris were characterized in two consecutive years and compared to the domesticated cultivars ‘Plavac mali’, ‘Merlot’ and ‘Xinomavro’. Five anthocyanidin-3-monoglucosides and their corresponding five 3-(6-O-acetyl) and five 3-(6-O-coumaryl) derivatives were identified and quantified using HPLC-DAD. Most wild grape samples had both acylated and non-acylated anthocyanin monoglucosides, although two individuals lacked acylated forms. DpGl were a greater percentage of the total in wild grape than in ‘Plavac mali’, ‘Merlot’ or ‘Xinomavro’. Principal component analysis showed differentiation of sylvestris from vinifera by anthocyanin profile. The anthocyanin profiles of sylvestris genotypes from the eastern Adriatic region, here presented for the first time, suggest genetic diversity within sylvestris in anthocyanin synthesis.