During his reign (781–806) the capital of Japan was moved from Heijōkyō in Nara, first to Nagaoka, and then to Heian. This marks the beginning of the Heian era in Japanese history. He was an active emperor who set up new government organisations and fought the Ezo tribes in the north of the country.
Earlier Imperial sponsorship of Buddhism, beginning with Prince Shōtoku (574–622), had lead to a general politicization of the clergy, along with an increase in intrigue and corruption. In 784 Kanmu shifted his capital from Nara to Nagaoka in a move that was said to be designed to edge the powerful Nara Buddhist establishments out-of-state politics—while the capital moved, the major Buddhist temples, and their officials, stayed put. Indeed there were a steady stream of edicts issued from 771 right through the period of Kukai's studies which, for instance, sought to limit the number of Buddhist priests, and the building of clan temples. However the move was to prove disastrous and was followed by a series of natural disasters including the flooding of half the city. In 785 the principal architect of the new capital, and royal favourite, Fujiwara no Tanetsugu, was assassinated.
Meanwhile, Kanmu's armies were pushing back the boundaries of his empire. This led to an uprising, and in 789 a substantial defeat for Kanmu's troops. Also in 789 there was a severe draught and famine—the streets of the capital were clogged with the sick, and people avoiding being drafted into the military, or into forced labour. Many disguised themselves as Buddhist priests for the same reason. Then in 794 Kanmu suddenly shifted the capital again, this time to Heian-kyō, which is modern day Kyoto. The new capital was started early the previous year, but the change was abrupt and led to even more confusion amongst the populace.
Politically Kanmu shored up his rule by changing the syllabus of the university. Confucian ideology still provided the raison d'être for the Imperial government. In 784 Kanmu authorised the teaching of a new course based on the Annals of Spring and Autumn based on two newly imported commentaries: Kung-yang, and Ku-liang. These commentaries used political rhetoric to promote a state in which, the Emperor as "Son of Heaven", should extent his sphere of influence to barbarous lands, thereby gladdening the people. In 798 the two commentaries became required reading at the government university.
Kanmu was the son of Emperor Kōnin. According to the Shoku Nihongi, (続日本紀), Emperor Kanmu's mother Yamato no Niigasa, later Takano no Niigasa, was a descendant of King Muryeong of Baekje, Korea. Kanmu was born before his father ascended to the throne.
After his father Kōnin became emperor, Kanmu's half brother was appointed to the rank of crown prince. But instead of his half brother, it was Kanmu who was later named to succeed their father.
Later, when he ascended to the throne, Kanmu appointed his young brother, Prince Sawara, whose mother was Takano no Niigasa, as crown prince. Prince Sawara was later expelled and died in exile.
Kanmu had many consorts and concubines, and as a result he had many sons and daughters. Among them, three sons would eventually ascend to the imperial throne: Emperor Heizei, Emperor Saga and Emperor Junna.
Some of his descendants (known as the Kanmu Taira or Kanmu Heishi) took the Taira hereditary clan title, and in later generations became prominent warriors. Examples include Taira no Masakado, Taira no Kiyomori, and (with a further surname expansion) the Hōjō clan. The waka poet Ariwara no Narihira was one of his grandsons.
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