Polymorphism at the single copy RPB2 locus was investigated to define the relationship between wild and domesticated grapevines. Two different forms still coexist in Eurasia, the cultivated (Vitis vinifera L. ssp. vinifera) and the wild (Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi), referred to as separate subspecies. Using the observed number of mutations at the RPB2 locus, as well as archaeological data, to define an approximate age of domestication, we have estimated a high nucleotide substitution rate (4.25 × 10⁻⁷) in the domesticated group. Moreover, the dynamics of population size in the RPB2 gene were estimated using Bayesian coalescent inference. The Bayesian skyline plot offered interesting information on the past dynamics of RPB2 for both wild and domesticated groups. The signal of exponential growth observed in grapevine accessions can be viewed as a consequence of human breeding activity during the domestication of the species. However, a recent and drastic decline of population size has been observed in the Mediterranean wild lineages. This event mirrors the demographic decline of wild grape, probably explained by anthropogenic pressure on its natural habitats and by the introduction of pathogens from North America in recent centuries.