From the 6th-century introduction of Buddhism, native Shinto and foreign Buddhism fused into a unified religious system. By the Nara period, shrines housed "jinguji" (temples for gods) and temples housed "chinjusha" (shrines protecting Buddhas). In the Heian period the "honji suijaku" theory emerged: Japanese kami were manifestations (suijaku) of buddhas and bodhisattvas descending to save the people. Amaterasu was identified with Dainichi Nyorai, Hachiman with Amida, and so on. Through medieval Ryobu Shinto (Shingon-based), Sanno Shinto (Tendai-based), and early modern Yoshida Shinto, and into Edo-era parish unity of shrines and temples, syncretism shaped Japanese religious life for 1,200 years until the 1868 separation edict. Traces remain everywhere—Yakushi-do at Tsurugaoka Hachimangu, the unified Rinnoji-Toshogu complex at Nikko.

The Genpei War (1180-1185) was a nationwide civil conflict between the Minamoto (Genji) and Taira (Heike) clans. Beginning with Minamoto Yoritomo's uprising at Ishibashiyama, the war culminated in the annihilation of the Taira at Dan-no-ura in 1185. Chronicled in The Tale of the Heike, the war's themes of impermanence (muōjō) profoundly influenced Japanese literature and culture. Its conclusion led directly to the founding of the Kamakura shogunate and the beginning of samurai governance.

In 1185, after the Minamoto clan destroyed the Taira at Dan-no-ura, Minamoto no Yoritomo secured imperial authorization to appoint military governors (shugo) and land stewards (jitō) throughout Japan. Though Yoritomo's formal appointment as Sei-i Taishōgun came in 1192, the year 1185 is now generally considered the effective founding of the Kamakura shogunate — inaugurating nearly 700 years of samurai rule in Japan.