The clan moved its seat from Kai to Mutsu Province in the early Muromachi period, and were confirmed as daimyō of Morioka Domain under the Edo-period Tokugawa shogunate.

During the Boshin War of 1868–69, the Nanbu clan fought on the side of the Ōuetsu Reppan Dōmei, supporting the Tokugawa regime.

In the Meiji period, the former daimyō became part of the kazoku peerage, with Nanbu Toshiyuki receiving the title of hakushaku (count).

Minamoto no Yoshimitsu was awarded Kai Province following the Gosannen War, and his great-grandson Nobuyoshi took the surname Takeda.

[1] Nanbu Mitsuyuki joined Minamoto no Yoritomo at the Battle of Ishibashiyama and served in various mid-level positions within the Kamakura shogunate and is mentioned several times in the Azuma Kagami.

He accompanied Yoritomo in the conquest of the Hiraizumi Fujiwara in 1189, and was awarded with vast estates in Nukanobu District the extreme northeast of Honshū, building Shōjujidate Castle in what is now Nanbu, Aomori.

Nanbu Motoyuki established Ne Castle, which was intended to be a center for the imperial government administration in the area.

Although the Nanbu clan by the time of the 24th hereditary chieftain Nanbu Harumasa controlled seven districts of northern Mutsu province (Nukanobu, Hei, Kazuno, Kuji, Iwate, Shiwa and Tōno), the clan was more of a loose collection of competing branches without strong central authority.

In 1590, the Sannohe faction led by Nanbu Nobunao organized a coalition of most of the Nambu clans and pledged allegiance to Toyotomi Hideyoshi at the Siege of Odawara.

[13] The clan's first direct encounter with foreigners came in the late 16th century, when a Dutch ship, the Breskens, arrived in Nanbu territory.

[15] On September 23, 1868, the Nanbu clan's troops joined in the attack on the Akita Domain, which had seceded from the alliance and sided with the imperial government.

[23] After the war, the Nanbu clan's holdings were drastically reduced by the imperial government as punishment for siding with the northern alliance.

[24] In the early years of the Meiji era, the main Nanbu line was ennobled with the title of count (hakushaku) in the new peerage system.