They are located at 3-7-1 Hakusan, Bunkyō, Tokyo, Japan, and open daily except Mondays; an admission fee is charged.

The Tokugawa shogunate opened two gardens in 1638 in Azabu and Ōtsuka neighborhoods of Edo for the purposes of growing medicinal herbs.

In 1684, the Azabu gardens were abolished and relocated to Koishikawa, to the site of a villa owned by Shogun Tokugawa Tsunayoshi.

In 1877, after the Meiji Restoration, the gardens became a part of Tokyo Imperial University and was the birthplace of Japanese botanical research.

Notable outdoor collections include camellias, cherries, maples, Japanese primroses, bonsai trees, and alpine plants.