Mizoguchi Hidekatsu was a general under Oda Nobunaga and subsequently Toyotomi Hideyoshi. He distinguished himself at a number of battles and was rewarded with a 60,000 koku holding in Echigo Province. During the Battle of Sekigahara, he sided with Tokugawa Ieyasu; however as Echigo Province had many supporters and former retainers of the Uesugi clan, he was ordered to remain in Echigo on guard duty. After the establishment of the Tokugawa Shogunate, he was confirmed in his existing holdings, which extended across the Echigo Plain between the Agano River and the Shinano River. This area, which stretched from eastern Niigata City, through Agano, Kamo and Minamikanbara District was excellent rice land, and the actual revenues of the domain were far in excess of its official kokudaka.
The second daimyō of Shibata, Mizoguchi Nobukatsu, split a 12,000 koku holding off of the domain for his younger brother, creating Sōmei Domain (沢海藩, Sōmei han), which lasted to 1687. The kokudaka of the domain was reduced from 60,000 to 50,000 with the remaining 2,000 coming from new rice lands developed within the domain. Nobukatsu was very active in developing new lands, and an additional 15,500 koku were splint amongst his three younger sons on his death, leaving the main 50,000 koku holding intact for his heir. The 8th daimyō, Mizoguchi Naoyasu established a Han school and invited noted gardeners from Edo and Kyoto as part of his rebuilding of the castle town. The 10th daimyō, Mizoguchi Naoaki, successfully petitioned the shogunate for an increase in kokudaka from 50,000 to 100,000 koku, although there was considerable debate within the domain as to whether or not the increased taxation was worth the increase in prestige and status.
During the Boshin War, the 12th daimyō, Mizoguchi Naomasa joined the Ōuetsu Reppan Dōmei; however, there was extensive opposition within the domain, and he was forced to quickly switch sides to the imperial cause.
As with most domains in the han system, Shibata Domain consisted of several discontinuous territories calculated to provide the assigned kokudaka, based on periodic cadastral surveys and projected agricultural yields.[4][5]