The wild boar, Sus scrofa, is an important game species widely distributed in Eurasia. Whereas the genetic variability of most European wild boar populations is well known, the status of wild boar living in Southern Italy is not as clear. We evaluated the present and past genetic diversity (D-loop, mtDNA) of the South Italian population, comparing it with that observed in other Mediterranean glacial refugia. Italian population showed highest genetic variability, if compared to other two European refugia (Iberian and Balkan). Most of samples from Italy carried sequences belonging to the European E1 haplogroup (80.9%) with a small proportion of the private Italian E2 (10.2%) and
of the Asian (8.9%) ones. Italian samples carrying an Asian haplotype were genotyped by MC1R nuclear gene, failing to disclose a recent introgression from domestic pigs. Mismatch distribution analysis of the Italian population was affected by secondary contacts between these different lineages. This genetic melting pot was detected since the Mesolithic and the Neolithic age, during which we found samples belonging to the indigenous Italian and European haplogroups. Further, a Near-Eastern haplotype was found in 1800 AD samples from Southern and Central Italy. Our results can be in agreement with post-glacial recolonization theories, as well as with the long history of human-mediated translocations of Sus scrofa in the Mediterranean basin.