With the establishment of the Tokugawa shogunate, Kuki Moritaka was confirmed as daimyō of Toba, initially with a kokudaka of 35,000 koku, growing to 55,000 koku under his son Kuki Hisataka, who was transferred to Sanda Domain in Settsu Province in 1632.

[1] The Kuki were replaced by a cadet branch of the Naitō clan, which ruled Toba until Naito Tadakatsu was forced to commit seppuku after killing fellow daimyō Nagai Naonaga in 1680.

[1] During the Boshin War, the domain remained loyal to the Shogunate and its forces fought in the Tokugawa army during the Battle of Toba-Fushimi.

After the Tokugawa defeat, the domain defected to the Imperial side, and as a result was fined heavily by the Meiji government.

[1] As with most domains in the han system, Toba Domain consisted of several discontinuous territories calculated to provide the assigned kokudaka, based on periodic cadastral surveys and projected agricultural yields.