The temple's founding story traces back to 737 or 741 AD, when the monk Gyoki is said to have established the site at the request of Emperor Shomu. No documentary evidence confirms this, and the true origins likely involve the Hata clan, a powerful immigrant family active in Japan since the Kofun period who controlled this corner of Omi Province. What is certain is that the monk Ennin revived the temple and brought it into the Tendai Buddhist sect during the Kajo era of 848 to 851, early in the Heian period. The temple grew through the centuries that followed, accumulating Buddhist statues from the late Heian through the Kamakura periods. By the Kamakura era, it had become a center for ecumenical scholarship, blending Tendai and Shingon traditions in an unusual cross-sectarian study.

The current Main Hall stands as a monument to national survival. Sasaki Yoritsuna, the military governor of Omi Province, commissioned its construction to mark Japan's successful defense against the Mongol invasions. Metal fittings on the altar bear the date 1288, and historical documents confirmed the commemorative purpose. But the building itself holds a surprise: when the cypress-bark roof was repaired in 1988, investigators discovered that the structure was actually built during the later Namboku-cho period -- the mid-fourteenth century -- and that the 1288 metal fittings had been salvaged from an earlier building and reused. The hall is a seven-by-seven-bay structure, large and dignified, with an inner chapel whose hipped-and-gabled roof shelters the temple's most sacred object: the honzon, a roughly carved figure of Kannon Bosatsu attributed to Gyoki. The carving appears almost unfinished, its surfaces bearing the raw marks of the chisel, but this is deliberate -- it belongs to a genre called 'hatchet statuary' from the latter Heian period, where the rough stroke was the art.

Oda Nobunaga's campaign against Tendai warrior monks targeted Mount Hiei and its affiliated temples across the region. Kongorin-ji received the attack, and its main gate area was damaged. But the layout of the temple worked as an unintentional defense: the central buildings sat deep within the compound, far enough from the entrance that the destruction did not reach them. The Edo period brought peace but also slow decline. The three-story pagoda, traditionally dated to 1246 but stylistically from the Namboku-cho period, deteriorated severely during the Meiji era and was eventually allowed to collapse into ruin. The Niten-mon gate suffered similarly, losing its entire upper story. Restoration would not come until the modern era -- the pagoda was repaired between 1975 and 1978, with artisans using a similar pagoda at neighboring Saimyo-ji in Kora as their reference model.

On February 1, 1868, two men met within the temple grounds to plan the overthrow of the Tokugawa shogunate. Saigo Takamori, the great warrior-statesman of Satsuma Domain, and Iwakura Tomomi, a court noble turned revolutionary, chose this remote temple to organize the Sekihotai militia. Within months, the shogunate would fall and Japan would enter the Meiji era. The temple that had survived Nobunaga's fires now served as a cradle for the birth of modern Japan. Both the pagoda and the Niten-mon gate carry Important Cultural Property designations today, the hall that sheltered conspirators bearing its layers of history with quiet dignity.

The Myoju-in, a subsidiary chapel of Kongorin-ji, burned in a fire in 1977 and has since been rebuilt. But its gardens survived, and they represent three distinct eras of Japanese garden design arranged in a single complex designated as a National Place of Scenic Beauty. The oldest garden dates from the Momoyama period, centered on a stone bridge with a Kamakura-era hokyointo stone pagoda. The second garden is from the early Edo period, dense with carefully placed stones. The third, from the middle Edo period, features a pond with a stone at its center shaped to evoke a ship. Walking the sequence is like moving through time -- each garden reflecting the aesthetic priorities of its century, from the bold martial confidence of the Momoyama era to the contemplative refinement of the later Edo period.