During the early modern period, Shugendo was split into the 'Honzan school' and 'Tozan school' by the Edo bakufu (Japanese feudal government headed by a shogun), and Shogo-in Temple was a central temple of the Honzan school.
近世以降、修験道は江戸幕府の政策もあって「本山派」「当山派」の2つに分かれたが、聖護院はこのうちの本山派の中心寺院であった。