However, after Yoshimitsu ASHIKAGA, Seii Taishogun (literally, "great general who subdues the barbarians") of the Muromachi bakufu (Japanese feudal government headed by a shogun), was assigned to Genji choja in 1383 and at the same time took the posts of both Junnain Betto and Shogakuin Betto, Shogun of the Muromachi shogunate continued to take the two Betto posts.
しかし、永徳3年（弘和3年/1383年）に室町幕府征夷大将軍足利義満が源氏長者に任じられ、同時に淳和院と奨学院の別当を兼ねて、以後室町幕府将軍が別当を務めた。