In the late Heian period, Minamoto rivalry with the Taira culminated in the Genpei War (1180–1185 AD). The Minamoto emerged victorious and established Japan's first shogunate in Kamakura under Minamoto no Yoritomo, who appointed himself as shōgun in 1192, ushering in the Kamakura period (1192–1333 AD) of Japanese history. The name "Genpei" comes from alternate readings of the kanji "Minamoto" (源 Gen) and "Taira" (平 Hei).
The Kamakura Shogunate was overthrown by Emperor Go-Daigo in the Kenmu Restoration of 1333. Three years later the Kenmu government would then itself be overthrown by the Ashikaga clan, descendants of the Seiwa Genji who established the Ashikaga shogunate (1333 to 1573).
The Emperors of Japan bestowed noble surnames upon members of the imperial family who were excluded from the line of succession and demoted into the ranks of the nobility.<ref name=":3" /><ref name=":1" /><ref name=":2" /> In May 814, the first emperor to grant the surname "Minamoto" was Emperor Saga, to his seventh son—Minamoto no Makoto, in Heian-Kyō (modern Kyōto).<ref>Frederic, Louis (2002). Japan Encyclopedia. Cambridge, Massachusetts: Harvard University Press.</ref><ref name=":1">Template:Cite book</ref>Template:Rp<ref name=":2" /> The practice was most prevalent during the Heian period (794–1185 AD), although its last occurrence was during the Sengoku period. The Taira were another such offshoot of the imperial dynasty, making both clans distant relatives.<ref>Template:Cite book</ref>
The Seiwa Genji's fortunes declined in the Hōgen Rebellion (1156), when the Taira executed most of the line, including Minamoto no Tameyoshi. During the Heiji Disturbance (1160), the head of the Seiwa Genji, Minamoto no Yoshitomo, died in battle.<ref name=Sansom/>Template:RpTaira no Kiyomori seized power in Kyoto by forging an alliance with the retired emperors Go-Shirakawa and Toba and infiltrating the kuge. He sent Minamoto no Yoritomo (1147–1199), the third son of Minamoto no Yoshimoto of the Seiwa Genji, into exile. In 1180, during the Genpei War, Yoritomo mounted a full-scale rebellion against the Taira rule, culminating in the destruction of the Taira and the subjugation of eastern Japan within five years. In 1192, he received the title shōgun and set up the first bakufu in the history of Japan at Kamakura—Kamakura shogunate.<ref name=Sansom/>Template:Rp
The protagonist of the classical Japanese novel The Tale of Genji (The Tale of Minamoto clan)—Hikaru Genji, was bestowed the name Minamoto for political reasons by his father the emperor and was delegated to civilian life and a career as an imperial officer.
Even within royalty there was a distinction between princes with the title Template:Nihongo3, who could ascend to the throne, and princes with the title Template:Nihongo3, who were not members of the line of imperial succession but nevertheless remained members of the royal class (and therefore outranked members of Minamoto clans). The bestowing of the Minamoto name on a (theretofore-)prince or his descendants excluded them from the royal class altogether, thereby operating as a reduction in legal and social rank even for ō-princes not previously in the line of succession.
Many later clans were formed by members of the Minamoto clan, and in many early cases, progenitors of these clans are known by either family name. There are also known monks of Minamoto descent; these are often noted in genealogies but did not carry the clan name (in favour of a dharma name).
There were 21 branches of the clan, each named after the emperor from whom it descended. Some of these lineages were populous, but a few did not produce descendants.
Saga Genji
The Saga Genji are descendants of Emperor Saga. As Saga had many children, many were bestowed the uji Minamoto, declassing them from imperial succession. Among his sons, Makoto, Tokiwa, and Tōru took the position of Minister of the Left (sadaijin); they were among the most powerful in the Imperial Court in the early Heian period. Some of Tōru's descendants in particular settled the provinces and formed buke. Clans such as the Watanabe, Matsuura, and Kamachi descend from the Saga Genji.<ref name=":0">Template:Cite book</ref>
Minamoto no Anbō (secular name Minamoto no Shitagō), great-grandson of Tōru
Watanabe no Tsuna (his official name was Minamoto no Tsuna, who resided at Watanabe in Settsu province, and took the name of the place), great-great-grandson of Tōru
These were descendants of Emperor Yōzei. While Minamoto no Tsunemoto is termed the ancestor of the Seiwa Genji, there is evidence (rediscovered in the late 19th century by Hoshino Hisashi) suggesting that he was actually the grandson of Emperor Yōzei rather than of Emperor Seiwa. This theory is not widely accepted as fact, but as Yōzei was deposed for reprehensible behaviour, there would have been a compelling motive to claim descent from more auspicious origins if it were the case.
These were descendants of Emperor Kōkō. The great-grandson of his firstborn Prince Koretada, Kōshō, was the ancestor of a line of busshi, from which various styles of Buddhist sculpture emerged. Kōshō's grandson Kakujo established the Shichijō Bussho workshop.
These were descendants of Emperor Reizei. Though they are included among the listing of 21 Genji lineages, no concrete record of the names of his descendants made Minamoto is known to survive.
This line consisted solely of Emperor Go-Saga's grandson Prince Koreyasu. Koreyasu-ō was installed as a puppet shōgun (the seventh of the Kamakura shogunate) at a young age, and was renamed "Minamoto no Koreyasu" a few years later. After he was deposed, he regained royal status, and became a monk soon after, thereby losing the Minamoto name.
Template:Nihongo, a 14th-century epic poetry compiled of the struggle between the Minamoto clan and the Taira clan for control of Japan at the end of the 12th century in the Genpei War (1180–1185).