Mukōjima comes from the region's old name, Hyakkaen was chosen to mean "a garden with a hundred flowers that bloom throughout the four seasons".

In 1804, Sahara Kikū, a native of Sendai Domain and a wealthy dealer in antiques purchased land near the Sumida River called the "Taga Yashiki" and planted 360 ume trees given by his friends such as Ōta Nanpo and Shibutsu Ōkubo in emulation of the famous "umeyashi" plum gardens at Kameido.The garden was initially called the "Shin-Umeyashiki" or the "Hanayashiki", and was named the "Hyakkaen" in 1806.

Sahara established a literary salon, inviting poets and painters to his garden, which evolved between 1804 through 1830 to include collections of flora found in the ancient Japanese poetry such as the Man'yōshū and in the Chinese Shi Jing to provide inspiration.

Over thirty stone monuments were erected in various locations around the gardens, inscribed with poems produced by members of this literary cortiere.

[1] However, with the rapid industrialization of the area following the Meiji restoration and the growing pollution of the water supply to the garden, it gradually fell into disrepair.