For his role in the Siege of Osaka, Hori Naoyuki, the 4th son of the famous general Hori Naomasa, was granted 5,500 koku holding in Echigo Province July 1616. He built a jin'ya in Shiiya to administer his new domain. Naoyuki's son Hori Naokage, served as Edo bugyō and Jisha-bugyō in the shogunal administration, and for which he was awarded additional holdings with a kokudaka of 9,500 koku, to which he added an additional 2,000 koku of newly developed rice lands. This enabled him to qualify for the status of daimyō. He established his seat in Kazusa Province at Kazusa-Kariya Domain (1642-1668) in what is now part of the city of Isumi, Chiba. His son, Hori Naoyoshi, moved to Kazusa-Hachiman Domain (1668-1698) in what is now part of Ichihara, Chiba. Tori Naoyoshi's son Hori Naosada then moved the clan's seat to the original jin'ya in Echigo Province in 1698, which marked the official start of Shiiya Domain. The clan headquarters remained at Shiiya until the Meiji restoration; however, the daimyō remained in permanent residence in Edo and managed the domain as absentee landlords.
During the period of the 8th daimyō, Hori Akitomo, fiscal reforms were implemented; however, Akitomo was of weak constitution and was unable to see the reforms through. The domain was also hit hard by the Great Tenmei famine, which resulted in considerable peasant unrest.
As with most domains in the han system, Shiiya Domain consisted of several discontinuous territories calculated to provide the assigned kokudaka, based on periodic cadastral surveys and projected agricultural yields.[2][3]