The Nihonmatsu Domain was also the scene of a major battle of the Boshin War of the Meiji Restoration.

The area around Nihonmatsu was territory of the Hatakeyama clan during the late Kamakura and Muromachi periods.

However, following the Siege of Odawara (1590), Toyotomi Hideyoshi re-assigned the area to Aizu Domain under the rule of the Gamō clan.

Hideyoshi later reduced the holdings of the Gamō clan, giving Nihonmatsu and surrounding areas to Asano Nagamasa.

This change was very short-lived, as Aizu domain was then reassigned to the Uesugi clan, and their holdings were expanded to encompass Nihonmatsu.

The Gamō recovered Nihonmatsu, but the domain was soon beset by a variety of natural disasters, including a massive earthquake, bad weather and flooding, leading to crop failure and widespread famine.

This in turn led to a peasant revolt, and the Gamō clan was eventually dispossessed by the Tokugawa shogunate and sent to Iyo Province in Shikoku.

However, their efforts were complicated by increasing demands for military support from the shogunate in policing the northern frontier areas of Ezo.

Many peasants were forced to sell themselves into servitude to pay for the high taxation, leading to unrest and even a revolt by senior retainers.

They were assigned repair work on the Nikkō Tōshōgū, Zōjō-ji and various tasks by Tokugawa shogunate which proved a severe drain on their resources.

Despite efforts at fiscal and land reform, the domain was deeply in debt, which was complicated during the time of the 7th daimyō, Niwa Nagayoshi, when the Great Tenmei famine struck.

During the Bakumatsu period, the 10th daimyō, Niwa Nagakuni, was assigned to the defense of Edo Bay, and with the start of the Boshin War, joined the Ōuetsu Reppan Dōmei.

His successor, Niwa Nagahiro made peace with the imperial forces but with a domain reduced in status to 50,700 koku.

Upon entering Nihonmatsu Castle in 1644, he immediately embarked on a program to rebuild the surrounding jōkamachi.

Mitsushige was also noted as a patron of the arts, and especially favoured the Sekishū-branch of the Japanese tea ceremony.

He was the eldest son of Niwa Mitsushige, and was received in formal audience by Shōgun Tokugawa Ietsuna in 1653. he became daimyō in 1679 on the retirement of his father.

He was the younger brother of Niwa Nagatsugu, and was received in formal audience by Shōgun Tokugawa Tsunayoshi in 1684.

He was the eldest son of Niwa Takahiro and was received in formal audience by Shōgun Tokugawa Yoshimune in 1741.

After the deaths of his son and grandson, he reassumed the chieftainship of the Niwa clan in 1902, and also the kazoku title of shishaku (viscount).

Following the defeat of Nihonmatsu Domain during the Boshin War in 1868, Nagakuni was placed under house arrest in Tokyo by the new Meiji government, which also ordered him to retire.

Nagakuni formally adopted his son-in-law, Nagahiro who then became daimyō, with Nihonmatsu reduced to 50,700 koku (half of what it had previously held).

When the post of daimyō was abolished, Nagahiro remained as Imperial governor of Nihonmatsu until the abolition of the han system.

In 1884, with the creation of the kazoku peerage system, Nagahiro received the title of shishaku (viscount).