Koto-in was established in 1601 by Tadaoki Hosokawa. He was a famous warrior under Toyotomi Hideyoshi, studied Zen under the Daitoku-ji abbot, Seigan, and was a distinguished disciple of tea master, Sen no Rikyu. When Rikyu was ordered to commit suicide, he left many treasured possessions to Hosokawa. Koto-in is home to two famous tea houses, Shoko-ken (built by Hosokawa in 1628) and Horai. There is a famous wash basin made from a stone brought from the Imperial Palace in Korea.

The Hojo Garden is in the chisen kaiyushiki (garden which is designed around a pond) style and is said to have been designed in the early Edo (1600-1868) period by the monk Gyokuen, who was connected to garden master Kobori Enshu. The garden includes the Shinji-ike (Heart Character) Pond, the Aoi-an Teahouse, and the Tokugawa Gongendo Hall. The cherry blossoms in the spring, the fresh greenery in early summer, the reflection of the autumn foliage onto the Shinji-ike Pond, and the snowy scenery and clear air in the winter can all clearly be seen, and along with imposing view of the Higashiyama mountains in the background, the garden exudes the moods of the four seasons.