The Institute for Nature Study is located in Shirokanedai, a region of Tokyo that was created by marine erosion during a diluvial epoch some 200,000 to 500,000 years ago.

Although it is not known when the first humans settled this area, pottery and shell mounds from the mid-Jomon period (about 2,500 years ago) have been discovered here, suggesting that the region was already settled by this point.

In the Heian period (794-1185), it is thought that rice paddies were cultivated in the swampy lowlands of the Meguro and Shibuya Rivers, while gromwell, an essential ingredient in dyemaking, was grown in the broad plains above. With the start of the Muromachi period (1336-1573), the powerful clans of this area built mansions here; earthen walls found in Shirokanedai are believed to be the remains of these houses. Though the masters of these houses are unknown, the place name “Shirokanedai” first appears in records dated to 1559, and one Shinrokuro, a grandson of military commander Ota Dokan (1432-1486), is listed as the area's governor in period records. Moreover, legend has it that Shinrokuro was “rich in silver” (shirokane-choja).

In the Edo period, Shirokanedai came under the control of Zojoji, a Buddhist temple. In 1664, it became the villa of Matsudaira Sanukinokami Yorishige (1622-1695), lord of Takamatsu and elder brother of the shogun Tokugawa Mitsukuni (1628-1701). Some of the older, larger pines in the Institute for Nature Study's modern gardens are thought to have been among the very trees that grew in Matsudaira's garden.

In the Meiji period (1868-1912), the site was used as a gunpowder magazine, under the control of the Naval Ministry and Army Ministry. It was taken over by the Imperial Family Forests and Fields Bureau of the Imperial Household Ministry in 1917, whereupon it was renamed the Shirokane Imperial Estate.

The site passed to the Ministry of Education in 1949, whereupon it was designated a “national monument and historical landmark” and opened to the public as a national natural-education park. It obtained its current status as the Institute for Nature Study of the National Museum of Nature and Science in 1962.

Remains of the earthen wall of a feudal mansion