This study is a “model study” of how to apply the findings of molecular ecological studies to wildlife management, aimed at showing the importance of analyses integrating population genetics, space-time information and bioinformatics methods. We chose the Japanese wild boar (Sus scrofa leucomystax) in Tochigi Prefecture, Japan, because its captured area has been spreading in recent years. We used 72 adult individuals gathered by hunters in 2010. Three putative sub-populations were estimated using microsatellite DNA. Our study indicated that the individuals newly found in the northern area originated from other prefectures, not from different areas within the same prefecture, and no inobuta (crossbreeding with pigs) in the maternal line were found. Comparing the number of mutations obtained by a coalescent simulation with that obtained by mitochondrial DNA, suggested that an assumed native population in the eastern area of Tochigi Prefecture was actually not native. Habitat preferences of the putative sub-populations, estimated by a generalized linear model, were different from each other, which also suggested that the boar could adjust its habitat based on the characteristics of the local environment. Risk maps, estimated using MaxEnt, based on past questionnaire surveys and those based on microsatellite DNA were different from each other.