Unlike European and North American cities, where urban fabrics are clearly separated from the surrounding rural landscapes, Japanese cities have long been maintaining a legacy of including agricultural landscapes in urban fabrics. Modern urban planning theories have regarded such mixture of urban and rural landscapes as disordered and chaotic. However, agricultural landscapes may provide indispensable ecological functions, including microclimate control, biodiversity conservation, and renewable energy supply to cities and thus should be counted as indispensable components of urban systems. This paper argues the need for a paradigm shift in Japanese urban planning, from clear separation to an appropriate mixture of urban and rural landscapes, by considering ecological functions provided by agricultural landscapes remaining and emerging in urban fabrics.