The conservation of biodiversity in urban areas has become important topics in urban environmental policy, and that contributes not only to improve urban living environment but also to enhance of people's awareness of biodiversity. For this purpose, it is necessary to assess regional ecosystem continuously by biodiversity monitoring. However, there are few municipal governments which have implemented continuous biodiversity monitoring, due to mainly financial restrictions. Selecting indicator species is considered to be an effective way to implement continuous biodiversity monitoring and assess regional ecosystem within budget constraints. In this study, we surveyed 30 municipal governments which have conducting biodiversity monitoring in the Tokyo metropolitan area for clarifying the selection method of indicator species. As a result, it was revealed that selected indicator species tended to differ depending on the purpose of the monitoring, species identification skills of observers, and degree of urbanization. It was also found that collaboration with diverse stakeholders (such as scientists, engineers, public administrators, and citizens) is an effective way to select the appropriate indicator species for biodiversity policies promotion.