The morphometry of Vitis vinifera seeds from different archaeological sites was studied. Preservation status differed between sites. Non-invasive and quantitative image analysis based on elliptic Fourier analysis (EFA) established different morphological variations between populations. Molecular analysis was performed to study genetic relationships, using nuclear microsatellite SSRs markers with high polymorphism. Morphometric analysis of archaeological endocarp outlines and allelic profiles of endocarp tegument delineated the general species-specific qualities of the modern cultivar.