In Japan, there are two species of bear, the Asiatic black bear (Ursus thibetanus japonicas) and the brown bear (Ursus arctos). The Asiatic black bear inhabits the islands of Honshu and Shikoku in 19 recognized local populations. On the other hand, the brown bear inhabits only the Hokkaido and has 5 local populations. Both bears are known as a destructive animal as well as an umbrella species. Hence, their habitat estimation is significant. However, there is an obvious lack of information on the spatial distribution of species. Currently only low-resolution distributional maps (5 km by 5 km in a national scale) are available for two bears. Therefore, this study aims to estimate population size at local population levels on target two bears in Japan, based on the species’ geographic distribution model. From published data, we collected point data regarding species’ presence and absence records. Potential environmental predictors were stored in GIS at spatial scale of 100 m by 100 m, split into a train and a test dataset. Predictive distributional models were developed based on logistic regression models and MaxEnt model. Based on the known population density, population size was estimated for each local population. Our finding contributes the wildlife protection project plan as well as the Japanese National Biodiversity Strategy 2010.