Koishikawa Botanical Garden

Koishikawa Botanical Garden (小石川植物園) is a facility run by the University of Tokyo. This site is listed as a Place of Scenic Beauty.
In the 17th century, this site used to be the residence of Tokugawa Tsunayoshi, the domain lord who would later became the 5th shogun of the Tokugawa Shogunate. In 1684 this grounds were converted into a shogunate-run medicinal herb garden to provide commoners with herbs, and when the feudal times ended, it eventually became the Koishikawa Botanical Garden of Tokyo Imperial University (present-day Tokyo University).
Though it is rather small as a botanical garden, it has a Japanese stroll garden which originated in the feudal times.
It's a 15-minute walk from Myogadani Station of the Tokyo Metro Marunouchi Line, or a 10-minute walk from Hakusan Station of the Toei Mita Line.

Kyu-Tokyo Igakko

In the northwestern corner of the botanical garden, there is a half-Western-half-Japanese-style (known as Giyo-fu in Japan) wooden building constructed in 1876 on the Hongo campus of Tokyo University and relocated here in 1969. The reason it's "half" is that though its appearance is a Western-style one, it was built with traditional construction methods by domestic carpenters. This type of buildings began to be produced when local carpenters saw real Western-style buildings built by Western architects in large cities like Tokyo or Yokohama and imitated them with their skill, but disappeared when Japanese universities began to ship architects who can build real Western-style architecture.
This building was the main building of Tokyo Igakko (Tokyo Medical College) which later evolved into the medical faculty of Tokyo University. Now the building is used as the Koishikawa Annex of the University Museum of Tokyo University. It's a small museum which exhibits miniatures of famous architecture of the world and some other things.