The Southern Court (南朝, Nanchō) were a set of four emperors (Emperor Go-Daigo and his line) whose claims to sovereignty during the Nanboku-chō period spanning from 1336 through 1392 were usurped by the Northern Court. This period ended with the Southern Court definitively losing the war, and they were forced to completely submit sovereignty to the Northern Court. This had the result that, while later Japanese sovereigns were descended from the Northern Court, posterity assigns sole legitimacy during this period to the Southern Court.

The Southern descendants are also known as the "junior line" and the Daikakuji line (大覚寺統, Daikakuji-tō), Daikaku-ji being the cloistered home of Go-Uda, a Southern ruler. Because it was based in Yoshino, Nara, it is also called the Yoshino court (吉野朝廷, Yoshino chōtei).

The genesis of the Northern Court go back to Emperor Go-Saga, who reigned from 1242 through 1246. Go-Saga was succeeded by two of his sons, Emperor Go-Fukakusa and Emperor Kameyama, who took turns on the throne. This was because on his death bed in 1272, Go-Saga had insisted that his sons adopt a plan in which future emperors from the two fraternal lines would ascend the throne in alternating succession. This plan proved to be unworkable, resulting in rival factions and rival claimants to the throne.

In 1333, when the Southern Emperor Go-Daigo staged the Kemmu Restoration and revolted against the Kamakura shogunate, the Shōgun responded by declaring Emperor Kōgon, Go-Daigo's second cousin once removed and the son of an earlier emperor, Emperor Go-Fushimi of the Jimyōin-tō, as the new emperor. After the destruction of the Kamakura shogunate in 1333, Kōgon lost his claim, but his brother, Emperor Kōmyō, and two of his sons were supported by the new Ashikaga shoguns as the rightful claimants to the throne. Kōgon's family thus formed an alternate Imperial Court in Kyoto, which came to be called the Northern Court because its seat was in a location north of its rival.

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