Then, Yoshinao ISSHIKI gained the confidence of the eighth-generation shogun, Yoshimasa ASHIKAGA, but in the turmoil of the Onin War in 1467 the Isshiki clan belonged to the Western army led by Sozen YAMANA because the clan was opposed to Wakasa-Takeda clan, which belonged to the Eastern army led by Katsumoto HOSOKAWA; this resulted in the defeat of the Western army, and thereafter the clan gradually weakened.
その後、一色義直が第八代将軍・足利義政の信任を受けるが、1467年の応仁の乱では細川勝元の東軍に与した若狭武田氏との反目から山名宗全の西軍に与して敗れたため、次第に衰退の一途をたどるようになる。