Kyoto is an old city blessed with beautiful natural and cultural landscapes. With the long history of the various events and responses to them, Kyoto is expected to offer some insight into how to create a sustainable city with resilience relevant to its historical inheritances and biodiversity. In this paper, we attempt to describe some concepts of developments and responses that could mitigate the negative impact of urbanization on its biodiversity and ecosystem services. (1) Modern city planning considering natural amenities as well as old Fengshui geomancy theory could conserve the surrounding mountains. Down-zoning and vistaed view preservation are examples.(2) Inside the city areas, the theory of island biogeography is applicable for biodiversity planning, and the size of the isolated greenery is the most important factor for species richness of all taxonomic groups. However, a single large patch is not always sufficient to conserve as many species as possible. Moreover, the heterogeneity of the environment, which is formed by its design and management, plays an important role in species richness. Japanese gardens and the created wildlife habitat park are good solutions for biodiversity. (3) The nature of rivers and wetland systems has been severely degraded in the urbanization process. However, the excellent Katsura detached palace garden and Oguraike wetland system, which were one-time national monuments with high biodiversity, suggest a smart adaptation to the increasing risk of flooding by climate change: ''Do you Kyoto''?