The Takatō Domain was dissolved in the abolition of the han system in 1871 by the Meiji government and its territory was absorbed into Nagano Prefecture.

[2] Following the Battle of Sekigahara in 1600, and the establishment of the Tokugawa shogunate in 1603, Hoshina Masamitsu, the grandson of Masatoshi, became the first Edo period daimyō of Takatō, and the domain was officially ranked at a kokudaka of 25,000 koku.

Masamitsu raised an illegitimate son of shōgun Tokugawa Hidetada as his own, under the name Hoshina Masayuki, and was rewarded with a 5,000 koku increase for his domain in 1618.

Following Hidetada's death in 1632, Masayuki was transferred to Yamagata Domain in Dewa Province in 1636, with an income of 200,000 koku.

The next lord, Torii Tadanori, however, died while under house arrest due to a scandal at Edo in 1689, leaving the clan's succession in the hands of the shogunate.

Tadanori's successor in the family, Torii Tadahide, was demoted to a 10,000 koku holding, Shimomura Domain in Noto Province.

The domain began to have financial troubles beginning under the following lord, Naitō Yorinori, who made efforts at reforms and innovations to solve the problems.

The Ejima-Ikushima affair occurred around the same time, resulting in the shogunal consort named Ejima, banished from Edo, being left in the custody of Takatō.

[5] Towards the Bakumatsu period, the final daimyō, Naitō Yorinao, established a han school and took part in the campaigns by the shogunate against Chōshū Domain.

During the 1868 Boshin War, however, Takatō sided with the newly founded Meiji government army against the last supporters of the shogunate and sent forces to fight in the Battle of Hokuetsu and the Battle of Aizu{[5] Naitō Yorinao remained governor of Takatō when the lands were formally handed over to the Emperor.

[6][7] Naitō Kiyokazu (内藤清枚, September 25, 1645 – May 29, 1714) was a daimyō in the early Edo period Tokugawa shogunate of Japan.

His appointment to the post of Osaka kaban in 1694 and 1707 and as sōshaban from 1695 to 1697 also required the outlay of capital, and from the start the domain was in a precarious financial situation.

However, he proved to be a poor choice, as he cared nothing for the administration of the domain, but spent his time hunting, organizing firework displays and on parties.