Despite of the large number of literature on genetic diversity of Sus scrofa in Europe, little is known about the genetic differences between wild boar populations in South (Kecel-Imrehegy) and Northern parts of Lake Balaton and the effect of the Lake to gene flow. Therefore, the study aims to establish genetic variability of wild boar populations between sampling site in Veszprém and Bács-Kiskun counties and to investigate effects of lake Balaton to gene flow. Earlier developed thirteen STR and sex identification microsatellite markers were used to amplify DNA isolated from 38 samples of wild boar populations between the hunting sites of Kecel-Imrehegy and North of Balaton (18 and 20, respectively). Result analysis showed low observes and Expected heterozygosity (Hobs=0.42±0.21 and H exp=0.45±0.25) and a low intrapopulation average gene diversity (Gdv= 0.35 and Gdv=0.4) for NorthBalaton and South Balaton Populations respectively. Plotting by PAST v2.17.c software failed to separate the two populations distinctively, however, it shows a small, non- significant difference. As expected we conclude that the two studied populations were genetically similar. This point out high gene flow between the populations despite being separated by Balaton and a long distance (150km apart) and hence no correlation between genetic and geographical distance.