Ampelographic descriptions, a set of 20 nuclear microsatellite loci (nuSSR), five chloroplast microsatellites (cSSR), as well as historical references have been used to identify 66 accessions of Vitis vinifera L. The plant material included major and minor varieties under risk of extinction, collected in the Balearic Islands, and now conserved in two germplasm repositories site in Spain. The 66 samples analyzed corresponded to 32 different genotypes, several unique genotypes were found, three of them remaining unknown. Some synonyms and homonyms were found in the Mediterranean basin, highlighting that the dispersal of some varieties are related with historical human movements and migrations occurred in three several periods, (1) around seventh century related to Islam expansion, (2) around thirteen to fifteenth centuries and (3) in the nineteenth century related to phylloxera crisis. Some parentages were identified, being the cultivar Callet Cas Concos a key variety in several crosses, confirming the high value of unknown varieties for parentage analysis. Several grouping methods confirm the existence of two gene pools.