Portugal has a long tradition in viticulture and a great number of grapevine cultivars. To analyze the genetic relations among wild vines from Portuguese populations and old Portuguese grapevine cultivars we use morphological traits and chloroplastidial microsatellites from 53 accessions of four distinct populations of Vitis vinifera L. ssp. sylvestris (Gmelin) and 57 accessions of Vitis vinifera L. ssp. vinifera from the Portuguese National Ampelographic Collection. Principal coordinate analyses with the scores obtain from the descriptors of both the accessions of sylvestris and vinifera vines revealed two groups. One group is formed by the wild vine population of Alcacer do Sal and three vinifera accessions Rufete, Seara Nova and Trincadeira das Pratas and a second group includes all the other wild vines and grapevine cultivars. A total of four different chlorotypes (A, B, C and D) are present in the vinifera accessions and two in the sylvestris accessions (A, B). Chlorotype A is the most frequent in all the plants analyzed and correspond to 75.4% of the grapevine cultivars and 66% of the wild vines. The mixed distribution of chlorotypes in the Portuguese cultivars and the predominance of chlorotype A both in its wild populations and cultivars reinforced the hypothesis that West Europe was a domestication center for Vitis vinifera L. ssp. vinifera.