Kinreizan Ryugenji is a Buddhist temple of the Soto-Zen, founded by Dogen Zenji (Soto-Zen Master 1200-1253),
who spread the practice of Shikantaza (Just Sitting Zen) to Japan and founded the Eihei-ji Temple.
In 1623, Uteji (Sakon) Mitsutaka was relocated to Yashima from his original home in the Namegata district (now called Itako) of Hitachinokuni,
in Ibaraki Prefecture. Uteichi received Hachise Sokuden Bunko Daiosho of Daikozan Chokokuji Temple as the founder of the temple,
having had good relations with him since his days in Namegata, and subsequently followed his disciple and successor Hakuho Kochin,
who established the temple which became the family temple for the Uteji clan.

However, in 1635, with Mitsutaka's son Mitsuhisa having died without leaving a successor, the Uteji clan had their territories seized.
The Sanuki Takamatsu Domain (currently the city of Takamatsu in Kagawa Prefecture) had been rated at over 170,000 koku,
but due to circumstances at the time, the feudal lord Ikoma Takatoshi, fourth-generation lord of the Ikoma clan,
had their lands attaindered by the shogunate, and transferred in 1640 to the Yashima Domain, which was rated at 10,000 koku.
Subsequently, the temple became the family temple for the Ikoma clan, which it remains to this day.
The Ikoma clan was a military family which served as one of the Sanchuro (arbitration offices) under Toyotomi Hideyoshi,
with lord Ikoma Chikamasa founding castles at Takamatsu and Marugame,
and having distinguished themselves in war - such as at the Battle at Shizugatake and Hideyoshi's Japanese invasions of Korea.

Thanks to those relationships, Yashima and the city of Takamatsu in Kagawa Prefecture share a sister city partnership.
Until the Meiji era, Ryugenji has experienced two separate fires.
In addition, after the entire temple burned down during the Boshin War in 1868,
the following reconstruction efforts occurred, over a long period of time, to the present day:

1876: Rebuilding of the KURI-the Temple Kitchen (temporarily serving as the Main Hall)
1880: Rebuilding of the Main Hall
1983: Rebuilding of the Ikoma clan mausoleum
1997: Rebuilding of the temple gate
2004: Rebuilding of the Rurido Hall
2015: Rebuilding of the New KURI-the Temple Kitchen (Kinryukaku)

In 2004,
the Main Hall, with its thatched roof, was registered as a Tangible Cultural Property by the Agency for Cultural Affairs, Government of Japan.