Wildlife management is important to resolve Human-Wildlife conflicts. The objective of this study is clarifying the relationship between animal distribution and ecological indicators which are various geo-information. In particular, we evaluated the difference of spatial scale (extent and grain size). Our target species are Asiatic black bear (Ursus thibetanus), Japanese macaques (Macaca fuscata), and Wild boar (Sus scrofa). Honshu (the Mainland of Japan) and Niigata Prefecture were defined for two types of spatial extent. For spatial grain size, 30 m and 500 m-spatial resolutions were performed in Niigata. Logistic regression was applied for predicting animal distributions. There is a similar tendency in the ecological indicator which affects distribution of all three species in Honshu scale. The ratio of broad-leaved forest and elevation were contributed as positive correlation, and cultivated area, urban, and water were contributed as negative. However, the predicted distribution of target animals were different. In Niigata, snow coverage was an important factor. Furthermore, ecological indicator was varied by the grain size. Both spatial extent and grain size were influenced the contribution of ecological indicators for animal distribution. We suggest that not only the importance of ecological indicators but also the effect of spatial scale is important for suitable management.