The clan claimed descent from Fujiwara Sumitomo (d. 941 AD), who settled in Iyo Province after the Tengyō no Ran war.

[3] Shortly afterwards, Toyotomi Hideyoshi invaded Kyushu and by quickly joining forces with him, the Arima were confirmed in their existing holdings.

However, after the start of the Edo period, Arima Harunobu fell from favour due to Tokugawa Ieyasu's aversion[4] to the Kirishitan faith - the term for the Roman Catholic religion in Japan.

Although his son, Arima Naozumi was married to an adopted daughter of Tokugawa Ieyasu, at the start of the suppression of the Kirishitan religion, he was transferred from Shimabara to Nobeoka Domain (53,000 koku) in Hyūga Province in 1614.

The Arima clan continued to rule Maruoka Domain until the Meiji restoration and abolition of the han system in 1871.