The Ii clan had been kokujin ryoshu (local samurai lords) of Iinoya, Totoumi Province for generations and Naomasa's grandfather (or one of Naomasa's family members) Naomori II died at the Battle of Okehazama, serving as a vassal of Yoshimoto IMAGAWA.
井伊氏は先祖代々、遠江国井伊谷の国人領主であり、直政の祖父（または一族）井伊直盛は今川義元に仕えて桶狭間の戦いで戦死した。