Bungo Province was under the control of the Ōtomo clan from the Kamakura period to the Sengoku period. Under the tenure of the Kirishitan warlord Ōtomo Sōrin, the Ōtomo clan was defeated by the Shimazu clan from 1586, and were confined to Nyūjima Castle (the predecessor of Usuki Castle). The Ōtomo were saved by Toyotomi Hideyoshi's 1586-1587 Kyūshū campaign and were allowed to reclaim Bungo province as their territory. However, Ōtomo Yoshimune (Sōrin's son) behaved in a cowardly manner during the Japanese invasions of Korea (1592–1598) which so angered Hideyoshi that he was deprived of his fief and banished. Bungo was divided into small fiefs, of which the 65,000 koku holding at Usuki was the largest. This was awarded to Ōta Kazuyoshi, who had a falling out with Ishida Mitsunari resulting in his being sidelined during the 1600 Battle of Sekigahara. He later died a monk in Kyoto. On the other hand, a general in the Western Army, Inaba Sadamichi, defected to Tokugawa Ieyasu's Eastern Army and achieved great military exploits at the Battle of Sekigahara, for which he was awarded 40,000 koku in Mino Province and 50,000 koku at Usuki in Bingo. Throughout the Edo period, the Inaba clan continued to rule Usuki for 15 generations.
The Inaba clan were classified as tozama daimyō as they became vassals of the Tokugawa after the Battle of Sekigahara. There was another branch of the Inaba who were fudai daimyō. Hayashi Masanari married Inaba Shigemichi's daughter, taking the "Inaba" surname. He later married Lady Kasuga, the wet nurse to ShogunTokugawa Iemitsu.
In Usuki, the 5th daimyō, Inaba Kagemichi, developed the jōkamachi of Usuki and the domain's administration. From the middle of the Edo period onward, the domain's finances became tight, and in 1830, the 12th daimyō, Inaba Terumichi, had debts exceeding 300,000 ryō. For this reason, in 1831, his retired father, Inaba Hiromichi, who had retained political power behind-the-scenes, carried out somewhat rough reforms such as thorough fiscal austerity and new rice field development, as well as the abandonment of old debts and negotiations for grace periods for repayments. As a result, the domain's finances improved considerably. In addition, all of the daimyō from the 11th daimyō, Takamichi onwards, either died young or had no heirs, so the domain was constantly on the edge of attainder as many succession notifications to the shogunate were by posthumous adoptions. In 1844, the domain supplemented its military by organizing a paramilitary force centered on farmers with rifles who had experience as hunters.
In the Bakumatsu period. the domain maintained neutrality, but in June 1869 Inaba Hisamichi was the first of the Bungo daimyō to return his domain registry to the Meiji government, and was appointed domainal governor. In 1871, due to the abolition of the han system, the domain became Usuki Prefecture, and was later incorporated into Ōita Prefecture. The Inaba clan was elevated to the kazoku peerage with the title of viscount in 1884.
Holdings at the end of the Edo period
As with most domains in the han system, Usuki Domain consisted of several discontinuous territories calculated to provide the assigned kokudaka, based on periodic cadastral surveys and projected agricultural yields, g.[4][5]