The grounds of Shinjuku Gyoen formed a part of the Takato domain Naito clan residence. The estate was bestowed upon hereditary vassal Kiyonari Naito when Tokugawa Ieyasu first entered Edo Castle. At the beginning of the Meiji Period (1868), the Naito Shinjuku Experiment Station was built on this site, with the aim of promoting agriculture. In 1897, it became Shinjuku Botanical Garden, which was set up as a garden for the then emperor who loved plants.