The founder of Kukishin-ryu, Yakushimaru Ryushin (薬師丸隆真), was born in 1318 in Hongu (in present day Wakayama prefecture), in an influential family that originated from the Fujiwara. As bettô, this family supervised the shrines in the area and during the Genpei war they commanded the Kumano Suigun.
After training in military skills and shugendô (mountain ascetism) within his clan, Ryushin studied esoterical Buddhism under the monk Jôkai of the Sanmaku-in temple in Kyoto and martial arts and onmyodo in Kurama-dera.
In 1335 he joined the forces of the Northern Court, commanded by AshikagaTakauji, in the battle against the Southern Court. After his fort at Mt. Hiei had fallen, Southern emperor Godaigo was treated so badly by Takauji, that Ryushin would supposedly have decided to help the emperor escape.
Together with some accomplices, he freed Godaigo from the palace where he was kept, after which they fled to Yoshino, persued by the troops of Takauji’s younger brother Tadayoshi.
On Kuragari pass the two sides clashed. After the blade of Ryushin’s naginata (or, according to other sources, his yari), was cut off in the confrontation, he fought on with the remaining shaft. Traditionally, this fight is considered the origin of the bo forms of Kukishin-ryu.
The group was saved by interference of reinforcements from Yoshino and Godaigo could proceed to safety at Mt. Kimpusen.
As thanks for his dedication, the emperor bestowed the family name Kuki on Ryushin. Ryushin taught his son UmanosukeTakayoshi and others within the clan and eventually the system came to be transmitted under the name Kukishin-ryu.
Militarily, the Kuki-clan remained active in the troublesome centuries that followed. With a fief that was situated on the coast of Kumano, they specialized in marine fighting. The Kumano suigun (Kumano Navy) became a feared force which, commanded by the 9th family head Kuki Yoshitaka, fought on the side of Oda Nobunaga and Toyotomi Hideyoshi.
In the 17th century, the tide turned against the clan, when an internal conflict over the succession of the 10th soke Moritaka resulted in the splitting of the area into the two smaller parts Ayabe-han and Sanda-han. In 1649 a competition was held in front of the Kukimitama-shrine, in which the head instructor of Kukishin-ryu in Ayabe-han, Hosoya Shinpachiro Yukihisa, was pitted against the swordmaster Tachibana Sagenta Kiyosada (橘左源太清定) from Tatebayashi-han. In the ensuing duel Hosoya killed his adversary with a single blow from his bokken (according to the tradition, he even managed to cut Sagenta up to his breast in half!).
Because the family that led the Tatebayashi-han was connected to the Tokugawa however, this outcome was very unfavorable indeed. By fleeing the Ayabe-han, Hosoya barely managed to save his skin, but it was henceforth illegal to practice Kukishin-ryu in the area.