But by the Bakumatsu period (1853-1868), the remaining territory controlled by the imperial house was about half of the interior of the region, and territorial relations among the villages had changed; the various villages in Yamaguni had joined together as organized parishioners of the same local shrine, the Yamaguni-jinja Shrine, and the new balance of power led to many conflicts over land control.
しかし幕末には禁裏御料は郷内の半分ほどで、村々の所領関係が異なることは、山国の諸村が一体となり山国神社の宮座を堅持していく上で問題も多かった。