The hybridization between wild boar and domestic pig has occurred since the first domestication event, and it still occurs until today both naturally or through human intervention. In this study, we used 13 Short Tandem Repeat (STR), 3 W Insertion or Deletion (InDel), and combination of both microsatellite loci to determine the genetic diversity and hybridization occurrence in several sites in Hungary that we divided into three different groupings.The genetic diversity analysis showed that all the population in this study was in deficit of heterozygosity and showed a small genetic distance between each population. However, the GENELAND analysis confirmed the genetic structuring in the populations, but the geographical clustering was not the source of it. The STRUCTURE analysis based on the combination of STR and W InDel markers could successfully provide evidence of the hybridization between domestic pigs and wild boars occurrence in Hungary, and the rate of the hybridization event was lower compared to the overall mean of hybridization occurrence in European Union reported.