The range of the Asiatic wild boar (Sus scrofa leucomystax) in Japan has rapidly expanded towards northern area of Japan over a decade. The expansion is possibly accounted for by recent changes in environments and population dynamics. Alternatively, artificial introduction of hybrids between wild boar and domestic pigs has been suggested. Our research objectives are to study genetic structures of expanding populations in Tohoku area, northern Japan, and to assess the level of introgression of domestic pig genes into native wild boar populations. Samples were collected mainly in Yamagata and Miyagi prefectures where wild boar populations have been expanding recently. We also collected samples from Fukushima, which is supposed to be a source population. The samples were genotyped at 7 microsatellite loci and subjected to Bayesian assignment tests using the software STRUCTURE 2.2. Mitochondrial DNA analysis was also conducted to determine phylogeographic relationship among local populations. Results showed that the expanding population of wild boars in the study area was separated into two geographic groups, apparently divided by mountains that served as geographic barriers. Gene introgression was suggested for several individuals, suggesting the current population structure was influence by human activities.