It was centered around Mori Jin'ya in what is now the town of Kusu, Ōita and was ruled by the tozama daimyō Kurushima clan for all of its history.

[1][2][3] Mori Domain was founded by Kurushima Nagachika (later called Yasuchika), who was a descendant of a branch of the Murakami pirates who dominated the Seto Inland Sea during the Sengoku period.

During the Battle of Sekigahara in 1600, he sided with the Western Army loyal to the Toyotomi clan; however, as his wife's uncle was Fukushima Masanori, he was able to obtain a pardon from Tokugawa Ieyasu through the assistance of Honda Masanobu and was relocated to a new fief in Bungo Province in 1601, with the same kokudaka.

In 1663, the third daimyō, Kurushima Michiyo, sailed from the domain's enclave of Tonari on Beppu Bay on sankin-kōtai, when he was caught in a storm in the Seto Inland Sea off the coast of Yashiro Island, Suō Province.

Throughout the Edo period, the Kurushuma clan continued to rule Mori Domain for twelve generations, without any transfer or reduction of territory.