There is now evidence that the Balkans and the other European peninsulas represent the most important genetic pools of game species, such as the wild boar (Sus scrofa). Wild boars captured or hunted in the Balkans are commercialized throughout Europe as live animals or meat. Management of genetic resources of this species needs a detailed description of the variability represented by different populations and integration of these data with their dynamics for a fruitful economic exploitation and sustainability. In addition, genetic characterization of different wild boar populations and domestic pig breeds in Europe can provide data useful for monitoring, identification and traceability of animals or meat, which makes it relevant in the forensic context. A particular problem related to wild boar is the need to avoid or monitoring genetic introgression from domestic pigs. This is important as wild boars can crossbreed with domestic pigs producing fertile hybrids, which presents both economical and ecological risks.