We examined the population genetic structure of the Asian black bear (Ursus thibetanus) in a large continuous habitat in northern Japan. To determine how population subdivision relates to management units (MUs) proposed by the Ministry of the Environment, genetic variation in the mitochondrial DNA control region (mtDNA-CR) and seven autosomal microsatellite loci was assessed in bears captured in southern Tohoku. Geographical distribution of the subpopulations was assessed using landscape analyses to find the best-fit model based on maximum entropy (MaxEnt) prediction and cost of movement. Genetic differentiation analyses revealed unique mtDNA-CR haplotypes in the study population. Bayesian population assignment of autosomal loci inferred four genetically distinct subpopulations in the study area (pop 1–4). The main distribution areas of pop1 and pop4 were separated by a high-cost zone for bear movement as a result of land use. Another high-cost zone was identified between pop2 and pop4, while the distribution of pop4 overlapped that of pop3. These results indicate that genetically distinct subpopulations are localized to areas that correspond roughly to MUs. The presence of subpopulations within an MU suggests that each MU is not always a single demographic unit.