He sided with Tokugawa Ieyasu at the Battle of Sekigahara against his nominal overlords, the Onodera clan, and was promoted to the status of a 10,000 koku daimyō, based at Hitachi-Fuchū Domain, with his holdings scattered between Dewa and Hitachi Provinces.
When the Mogami clan was dispossessed, the Tokugawa shogunate transferred him in 1623 from Hitachi to the newly created Honjō Domain, and increased his revenues to 20,000 koku, which were all consolidated in the form of 103 villages in Yuki County where his descendants ruled for 11 generations to the Meiji Restoration.
It was 11-days travel time from Edo, where the clan maintained its primary residence (kamiyashiki) at Kita-Inari-cho, in Shitaya.
During the Boshin War, the final daimyō of Honjō Domain, Rokugō Masakane sided with the Ōuetsu Reppan Dōmei; however, the domain had scant military resources and was quickly overrun by forces of the pro-Imperial Satchō Alliance, which destroyed Honjō Castle.
With the abolition of the han system in July 1871, and the absorption of Honjō Domain into Akita Prefecture, Rokugō Masakane relocated to Tokyo.