A City Biodiversity Index (CBI) has been proposed and applied at the international level to enable local municipalities and cities to manage biodiversity and ecosystem services in a sustainable manner. CBI databases are being constructed as global platforms, though the available dataset is limited. The land-use dataset is one of the datasets that can be utilized to apply the CBI on the national level in countries including Japan. To demonstrate the importance and potential of the CBI under the limitation of the available dataset, we attempted to apply the CBI to the 791 Japanese cities by using available land-use indicators, and categorized the cities based on the indicators. The focus of the CBI is self-assessment, but we propose that grouping of cities with similar profiles is possible and can serve as a basis for potential collaboration. Coordinating policies on various scales is necessary in order to enhance biodiversity on a global scale; one option is to increase collaboration among cities. As a result, we found three groups with similar characteristics amongst cities with forests, paddies, and croplands as major compositions in terms of biodiversity. These findings will contribute to policy formation and efficient information sharing for ecosystem services management.