Background: Magna Graecia is the ancient name used to label the area of South of Italy extensively populated by Greek colonizers. Archeological and historical evidences identified in this region the oldest winegrowing area in Italy, pointing out its importance in the spread of high specialized viticulture around the Mediterranean Sea shores. In this work, the genetic diversity of Magna Graecia grape germplasm was assessed and its role in the grapevine propagation around the Mediterranean basin was underlined. Results: A large collection of grapevines from Magna Graecia was compared with germplasm from Georgia up to the Iberian Peninsula by using the 18K SNP array. High level of genetic diversity of the analyzed germplasm was pointed out; clustering, structure analysis and DAPC (Discriminant Analysis of Principal Components) highlighted the genetic relationships among genotypes from South of Italy and Eastern Mediterranean Sea (Greece). A gene flow from East (Georgia) to West (Iberian Peninsula) was identified throughout the high number of admixed samples detected. Pedigree analysis showed a complex and well-structured network of first degree relationships, where the cultivars from Magna Graecia were mainly involved. Conclusions: This study provided evidence that Magna Graecia germplasm was shaped by historical events that occurred in the area due to the robust link between South Italian and Greek genotypes. The uniqueness of this ampelographic platform was mainly an outcome of a complex natural or man-driven crosses involving elite cultivars.