The main line of Kyoto-Ogasawara clan continued as Shogun's retainer, however, after Tanemori OGASAWARA died at Eiroku Incident in 1565, his son Hidekiyo (Shosai) OGASAWARA became a masterless samurai, but later he served the Hosokawa clan (the future Hosokawa clan of Kumamoto Domain).
京都小笠原氏の一族は、嫡流は幕臣として続いたが、小笠原稙盛が永禄8年（1565年）の永禄の変で将軍足利義輝とともに討死すると、稙盛の子の小笠原秀清（少斎）は浪人し、後に細川氏（後の熊本藩細川氏）に仕えた。