Introduction of the bullfrog Rana catesbeiana is considered detrimental to native fauna. However, methods for controlling bullfrog populations have not yet been established. Managing habitats to resist invasion is important for alien species that are difficult to control directly. We surveyed habitat characteristics of paddy fields in eastern Japan inhabited by bullfrogs and analyzed their microhabitat selection. Our results suggest that adult bullfrogs prefer microhabitat with deep water. Therefore, it may be possible to prevent invasion of adults by keeping water shallow. Managing local habitats to prevent immigration may reduce the spread of bullfrogs on larger spatial scales.