Minamoto no Mitsunaka was a real person. As depicted in The Accidental Samurai, Mitsunaka was loyal to a number of Fujiwara regents. While he profited a great deal from these connections, he was also loyal to most of the Emperors those regents served. He was an important Minamoto. The Minamoto were, as the book explains, relatives of the Emperor who were not close enough to be heirs to the throne and were given the honorary title, Minamoto. The Minamoto were broken into clans, or Genji, depending on what Emperor their clan descended from. Mitsunaka was a member of the powerful Seiwa Genji, who descended from Emperor Seiwa.
Several years after the events in The Accidental Samurai were set, Mitsunaka helped a Fujiwara regent force Emperor Kazan, Emperor Murakami’s grandson, to abdicate the throne so that the regent’s grandson could assume the throne. As in the novel, Mitsunaka had an estate in Tada, in Settsu province. It is not clear what his role in court politics was in 964, but we know that by 969 he was heavily involved with court politics and helped implicate Minamoto no Takaakira in a plot against the throne, which helped ingratiate him to Fujiwara power brokers.
Mitsunaka had three sons, one of whom, Minamoto no Yorimitsu, is a famous figure in Japanese folklore.