Despite the vast literature on genetic variation in the domestic pig Sus scrofa, little is known about genetic differentiation in wild boar populations. Here we present an up-to-date review of published data on the past and recent history of the European wild boar, its genetic diversity and the spatial distribution of genetic variation throughout the continent. The phylogeography of the species seems to be shaped mostly by past large-scale events (like postglacial recolonization) rather than by more recent human manipulation. Genetic differentiation is observed both on a continental and a regional scale, and non-intuitive barriers to gene flow occur. From an indirect estimate, hybridization between wild boar and domestic pigs is seemingly a minor source of genetic variation for wild boar populations, yet risks are still linked to the release of captive hybrids in some areas. Finally, we present future perspectives concerning the development of powerful molecular tools and their possible application to the study and management of this species.