The Genpei War was the culmination of a decades-long conflict between between the Taira and Minamoto clans during the late-Heian period of Japan over dominance of the Imperial court, and by extension, control of Japan. In the Hōgen Rebellion and in the Heiji Rebellion of earlier decades, the Minamoto attempted to regain control from the Taira and failed. In 1180, Taira no Kiyomori put his grandson Antoku (then only 2 years of age) on the throne after the abdication of Emperor Takakura.

Emperor Go-Shirakawa's son Mochihito felt that he was being denied his rightful place on the throne and, with the help of Minamoto no Yorimasa, sent out a call to arms to the Minamoto clan and Buddhist monasteries in May.

It seemed that the Minamoto revolt and thus the Genpei War had come to an abrupt end. In vengeance, the Taira sacked and burned the monasteries that had offered aid to the Minamoto. The monks dug ditches in the roads, and built many forms of improvised defenses. They fought primarily with bow & arrow, and naginata, while the Taira were on horseback, giving them a great advantage. Despite the monks' superior numbers, and their strategic defenses. Thousands of monks were slaughtered nearly and every temple in the city were burned to the ground, including the Kōfuku-ji and Tōdai-ji. Only the Shōsōin survived.

It was at this point that Minamoto no Yoritomo took over leadership of the Minamoto clan and began traveling the country seeking to rendezvous with allies. Leaving Izu Province and heading for the Hakone Pass, he was defeated by the Taira in the battle of Ishibashiyama. Yoritomo escaped with his life, fleeing into the woods with Taira pursuers close behind. However he successfully made it to the provinces of Kai and Kōzuke, where the Takeda and other friendly families helped repel the Taira army.

Yoritomo made it to the town of Kamakura, which was solidly Minamoto territory. Using Kamakura as his headquarters, Minamoto no Yoritomo sent his counselor, Hōjō Tokimasa to convince the warlords Takeda of Kai and Nitta of Kotsuke to follow Yoritomo's command as he marched against the Taira. As Yoritomo continued through the region below Mount Fuji and into Suruga Province, he planned a rendezvous with the Takeda clan and other families of the provinces of Kai and Kōzuke to the north. These allies arrived at the rear of the Taira army in time to ensure a Minamoto victory.

Taira no Kiyomori died from illness in the spring of 1181 succeeded by his son Taira no Tomomori. At around the same time, Japan faced a series of droughts and floods that destroyed the rice and barley crops in 1180 and 1181. Famine and disease ravaged the countryside; an estimated 100,000 died.

Minamoto no Yukiie was defeated by a force led by Taira no Shigehira at the Battle of Sunomatagawa. However, the "Taira could not follow up their victory."

Yoritomo grew increasingly concerned about his cousin's ambitions. He sent an army to Shinano against Yoshinaka in the spring of 1183, but the two sides managed to negotiate a settlement rather than fighting one another. Yoshinaka then sent his son to Kamakura as a hostage. However, having been shamed, Yoshinaka was now determined to beat Yoritomo to Kyoto, defeat the Taira on his own, and take control of the Minamoto for himself.

The Taira had conscripted a huge army, marching forth on May 10, 1183, but were so disorganized that their food ran out just nine miles east of Kyoto. The officers ordered the conscripts to plunder food as they passed from their own provinces, which were just recovering from the famine. This prompted mass desertions. As they entered Minamoto territory, the Taira divided their army into two forces. Yoshinaka won by a clever strategy; under cover of nightfall his troops enveloped the main body of the Taira, demoralized them by a series of tactical surprises, and turned their confusion into a disastrous, headlong rout. This would prove the turning point in the Genpei War in the favour of the Minamoto clan.

Minamoto no Yoshinaka sent an army to cross the Inland Sea to Yashima, but they were caught by the Taira just offshore of Mizushima (水島), a small island of Bitchu Province, just off Honshū. The Taira tied their ships together, and placed planks across them to form a flat fighting surface. The battle began with archers loosing a rain of arrows upon the Minamoto boats; when the boats were close enough, daggers and swords were drawn, and the two sides engaged in hand-to-hand combat. Finally, the Taira, who had brought fully equipped horses on their ships, swam to the shore with their steeds, and routed the remaining Minamoto warriors.

Minamoto no Yukiie tries and fails to recoup the loss of the battle of Mizushima. The Taira forces split into five divisions, each attacking in succession, and wearing down Yukiie's men. Eventually surrounded, the Minamoto were forced to flee.

Minamoto no Yoshitsune arrived soon afterwards with his brother Noriyori and a considerable force, driving Yoshinaka from the city. This was an ironic reversal of the first Battle of the Uji, only four years earlier. Yoshinaka's wife, the famous female samurai Tomoe Gozen, is said to have escaped after taking a head as a trophy.

Minamoto no Yoshinaka made his final stand at Awazu, after fleeing from his cousins' armies. With night coming and with many enemy soldiers chasing him, he attempted to find an isolated spot to kill himself. However, the story says that his horse became trapped in a field of partly frozen mud and his enemies were able to approach him and kill him.

The beginning of the battle consisted mainly of a long-range archery exchange, before the Taira took the initiative, using the tides to help them try to surround the enemy ships. They engaged the Minamoto, and the archery from a distance eventually gave way to hand-to-hand combat with swords and daggers after the crews of the ships boarded each other. However, the tide changed, and the advantage was given back to the Minamoto. One of the crucial factors that allowed the Minamoto to win the battle was that a Taira general, Taguchi Shigeyoshi, defected and attacked the Taira from the rear. He also revealed to the Minamoto which ship the six-year-old Emperor Antoku was on. Their archers turned their attention to the helmsmen and rowers of the Emperor's ship, as well as the rest of their enemy's fleet, sending their ships out of control. Many of the Taira saw the battle turn against them and committed suicide.

Key Findings:

1. The defeat of the Taira armies meant the end of Taira "dominance at the capital".
2. Minamoto Yoritomo formed the first bakufu and ruled as Japan's first shogun from his capital at Kamakura. This was the beginning of a feudal state in Japan, with real power now in Kamakura.
3. Rise to power of the warrior class (samurai) and the gradual suppression of the power of the emperor - This war and its aftermath established red and white, the colors of the Taira and Minamoto standards, respectively, as Japan's national colors.