Later Yoshimitsu ASHIKAGA became the first Genji Choja as Seiwa-Genji (Minamoto clan) to succeed the Bettoshoku of both Shogakuin and Junnain, and after that Seii taishogun (literally, "great general who subdues the barbarians") of the Ashikaga clan (shogun family in the Muromachi period) became Genji Choja many times, holding both of these offices.
のちに足利義満が清和源氏として初めて源氏長者になり両院別当を兼ね、以後もしばしば源氏長者になった足利氏征夷大将軍が兼務した。