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The Early Nine Year's War (前九年合戦 Zenkunen kassen ) erupted in 1051, when Minamoto no Yoriyoshi and his son Yoshiie arrived in the north, from Kyoto, as agents of the Imperial court. They were there to put an end to a conflict between the Governor of Mutsu province (which bordered the Kiyohara's Dewa) and the Chinjufu shogun (Defender of the North), Abe no Yoritoki. The Kiyohara Governor of Dewa contributed warriors to the Minamoto effort, and aided in their victory over the Abe clan, which was achieved in 1063.
The Kiyohara then took over the administration of Mutsu, along with Dewa. Within the next twenty years, quarrels and conflicts arose within the family over differing interests arising from intermarriage with different warrior families. Kiyohara no Masahira, Iehira and Narihira, heads of branches of the family, created such a disturbance that Minamoto no Yoshiie, who had taken the formerly Abe post of Defender of the North, felt it necessary to interfere in the conflict. In 1083, he was appointed Governor of Mutsu, and arrived in the north to attempt to resolve the situation peaceably; he soon was forced to resort to gathering his own troops. After much fighting, the violence came to an end; Iehira and his uncle Kiyohara no Takahira had been killed, the other Kiyohara leaders surrendered. Control of both Dewa and Mutsu then passed to Fujiwara no Kiyohira, an ally of Yoshiie.
The kuge branch continued their legacy of scholarship, spawning writers, scholars, poets and artists. The descendants possessed hereditarily the office of daigeki. Kiyohara no Yorinari (1122–1189), son of the Daigeki Kiyohara no Suketada, was governor of Etchu province and excelled in law, literature and history. The clan's Kyoto mansion, along with all the books and scrolls contained within, was destroyed in the Ōnin War of the late 15th century.
Kiyohara of note
- Kiyohara no Fukayabu
- Kiyohara no Motosuke
- Sei Shōnagon - daughter of Motosuke, and one of the most famous women poets in all of Japanese history
- Kiyohara no Natsuno - jurist of the 9th century
- Kiyohara no Takahira
- Kiyohara no Iehira
- Kiyohara no Masahira
- Kiyohara no Narihira
- Sansom, George (1958). 'A History of Japan to 1334'. Stanford, California: Stanford University Press.