The Kutsuki family's origins were in the Sasaki family, from which the Rokkaku also came. The Kutsuki estate would eventually be taken into possession by the Bakufu, and the Kutsuki family would thus serve under them. The Kutsuki and Rokkaku families had a capricious relationship: in 1487, the Rokkaku attacked Ashikaga Yoshihisa, and the Kutsuki sided with the latter in the ensuing battle. In later years, however, Kutsuki Mototsuna would work together with the Rokkaku, but in such a way that they treated each other as equals.

This brings us to Mototsuna himself. Born in 1549, Mototsuna was from Kutsukidani, in Omi. He served under many families, including the Rokkaku, the Asakura, Ashikaga Yoshiaki, and finally served under Oda Nobunaga following his submission to Hideyoshi in 1584. Despite being little known, he distinguished himself in many respects. When the Miyoshi attacked Kyoto, Mototsuna rushed to defend the shogun Yoshiaki. When Oda was attacked by the Asakura, Kutsuki assisted him in his escape back to Kyoto. He also served as a magistrate who tended to Hideyoshi's finances, and was in charge of the "Kenchi" (rice surveys) of Echizen. He served in the Odawara and Korean campaigns.

During the battle of Sekigahara, Kutsuki sided with the western army, but being prompted by Kobayakawa's troops, betrayed the cause and attacked Otani Yoshitsugu. This was not recognized by Tokugawa Ieyasu, who decreased his holdings from about 20000 koku in the Kutsuki area to 9200 koku. In 1616, he shaved his hair and became a monk, but lived until 1632.