The conservation of urban biodiversity has been promoted under international processes such as the Convention on Biological Diversity. Thus, municipal governments in Japan are each required to plan ecological networks in a "Green Master Plan” (GMP). In this study, we have discussed current trends and issues in methods of creating GMPs for the conservation of urban biodiversity, by examining 20 plans which had been selected as the best examples of excellence. Specifically, we aimed to answer the following questions: (1) How do the present GMPs deal with urban biodiversity? (2) What problems are there for conserving urban biodiversity by means of a GMP? (3)What kind of scientific knowledge can we apply in order to solve those problems? Our examination revealed that there are few GMPs in which an ecological network is planned concretely and effectively, and that there are several problems for each planning procedure. In addition, a variety of previous works on urban ecology in Japan was collected and looked at from the viewpoint of finding solutions for these problems. Future research tasks were then argued.