In 1594, Hideyoshi held a magnificent cherry blossom viewing party at Yoshino, bringing thousands of guests and using Yoshimizu-in (now Yoshimizu Shrine) as his grand headquarters. He had the garden specially arranged for the occasion. Held just after completing the unification of Japan, this celebrated hanami became legendary as a symbol of his supreme power and glory.

When Emperor Go-Daigo fled Kyoto and established the Southern Court at Yoshino, this hall — then known as Kissui-in — served as his first temporary palace. The shrine today enshrines both Go-Daigo and his loyal general Kusunoki Masashige. In 1336, shortly before the Battle of Minatogawa, Masashige made his final appeal to Go-Daigo in Kyoto, urging a negotiated settlement with the Northern Court; the emperor refused, and Masashige took his own life at Minatogawa soon after. Although Masashige died before Go-Daigo's flight to Yoshino and never set foot here himself, he is enshrined alongside the emperor in tribute to his loyalty to the Southern Court cause.