The domain was centered at Yoita Jin'ya, located in what is now part of the city of Nagaoka in Niigata Prefecture.
The Makino ruled for three generations, and were transferred to Komoro Domain in Shinano Province in 1689.
In 1705, Ii Naotomo, daimyō of Kakegawa Domain refused to participate in the mandatory sankin-kōtai to Edo, and was relieved of his office by the shogunate due to mental illness.
Normally, this would have been cause for attainder, but the shogunate took into account the role of the Ii clan in the early days of the shogunate, and allowed his adopted son, Ii Naonori to inherit, albeit with a reduction in kokudaka from 35,000 to 20,000 koku.
The following year Naonori was transferred from Kakegawa to Yoita, which lacked the status of a "castle-holding domain".
This cadet branch of the Ii clan continued to rule Yoita until the Meiji restoration.
Yoita resisted sending its own forces to fight in the Boshin War until the battle against Shōnai Domain, at which time it contributed 166 troops out of a samurai population of 253.
Under the new Meiji government, Ii Naoyasu was given the kazoku peerage title of shishaku (viscount), and later served as a member of the House of Peers.
He became daimyō in 1705 when his adopted father was relieved of his position by the Tokugawa shogunate due to mental illness and his refusal to go on the sankin kōtai to Edo.
The following year, Naonori was transferred from Kakegawa to Yoita in Echigo Province, which had an equal kokudaka, but did not have the prestige of a castle.
In 1715, he was ordered to serve as bugyō presiding over the 100th anniversary of Tokugawa Ieyasu's death at the Nikkō Tōshō-gū.
Naokazu was the eldest son of Kimata Moriyoshi, the karō of Hikone Domain.
During his career, he served as bugyō presiding over the Shogunal pilgrimage to Nikkō Tōshō-gū and to one of the Joseon missions to Japan.
He rebuilt Yoita jin'ya to more resemble a castle, in line with the improved prestige of the domain.
He was remembered as a good ruler, rebuilding the domain after damage caused by the 1828 Sanjō earthquake and reconstructing many Buddhist temples and Shinto shrines.
Naoyasu was born in Edo as the fourth son of Ii Naosuke of Hikone Domain.