The origins of viticulture and the domestication of the grapevine have been the subject of much research, notably on the basis of archaeobotanical remains. To identify wild and domesticated grapevines, analyses using various measurements have been performed on archaeological grape pips: length and breadth of the pip, length of the stalk, placement of the chalaza and indices/formulas involving these measurements. The performances of traditional methods based on size parameters, however, can vary largely when applied to modern cultivars. In addition, recent studies on the morphological distinction between wild and domesticated grape pips using size measurements and ratios highlighted the importance of the comparisons between the archaeological material to a representative reference collection of grape pips from diverse modern cultivars and wild populations. Given that different methods have been proposed for the distinction between wild and domesticated grape pips, some based on measurements and others on shape, this paper tests for the first time these methods based on a standardized collection of modern pips and compares their performances. The analyses were performed on a set of modern reference grape pips consisting of 34 cultivated varieties and 13 wild genotypes. Then, archaeological grape pips were compared to this set of modern reference material using the same measurements and methods. We used grape pips from three sites located in Northern and Southern Greece and dated from the Late Neolithic (ca. 4500-4000 BC) to the Late Middle Bronze Age (ca. 1700-1620 BC): Dikili Tash, Tzoungiza and P.O.T.A. Romanou. Our results show that shape analysis is the most efficient method to identify wild and domesticated grapevines, while traditional measurements are also highly reliable. The Stummer index represents the least accurate method. According to our analyses of the archaeological pips from Late Neolithic and Early Bronze Age Greece belong to the wild morphotype. The EBA assemblage from Tzoungiza offers the first reliable evidence of morphologically domesticated grape pips, but the relative proportions of each type vary according to the methods used. This clearly shows how narratives about the origins of early viticulture and grapevine domestication may be influenced by the choice of identification method applied to archaeological grape pips.