A great part of the history of Shorin-ji Temple up until the modern times remains unclear, but it is thought that it had close relations with Omiwa-jinja Shirine along with Myoraku-ji Temple.
聖林寺の近世までの歴史は不明の部分が多いが、妙楽寺とともに、大神神社（おおみわじんじゃ）とも関連が深い寺院であったと思われる。