Socio-economic changes have been the main cause of the change in forest vegetation in Japanese rural landscapes over the past 40 years. In the Ota River basin of southwestern Honshu, Japan, farmers and local people seldom use rural/secondary pine and oak forests, and owners have tended to manage densely planted conifer plantations less intensely. Moreover, pine wilt disease has recently killed pine trees over a large proportion of the lower altitude zone in this basin. It is important to establish functional forests in this basin, and restoring the natural forest ecosystem is one appropriate option for sound landscape construction. This study analyzed the geotope (topography and geology) preference of biotope (vegetation) in the Ota River basin using Jacobs' index. The natural vegetation was distributed in a specific narrow geotope zone and we clarified the potential distribution of the natural vegetation zone. Secondary vegetation was widely distributed in this potential natural vegetation area.