After the extinction of Imperial Prince Morisada's family line, the temple was also the palace in which both Emperor Gosaga and Emperor Gofukakusa resided following their abdications, and it is for this reason that the family line of Emperor Gofukakusa took the name surname 'Jimyoin' (just as the name of the opposing Emperor Kameyama's family line was changed to 'Daikakuji' because he resided at Daikaku-ji Temple following his retirement).
守貞親王系が断絶後も後嵯峨天皇・後深草天皇が退位後の御所に定められたことから、後深草天皇の系統を後に持明院統と称した（対立関係にあった亀山天皇の系統を大覚寺統と呼ぶのも亀山天皇が退位後に大覚寺に住んだ事に由来している）。