The first record that mentions the Yagyu clan is about Nagayoshi YAGYU (Muneyoshi YAGYU) who was believed to be a child of Daizen no suke (person who was in charge of meals in the Imperial Court) Nagaie YAGYU in the period of the Northern and Southern Courts (Japan); and according to a genealogy of the Yagyu clan "Gyokuei Shui," Nagayoshi supported the Southern Court and fought against the forces of Nagatoki HOJO and Tokimasu HOJO who had their base at Rokuhara Tandai (an administrative and judicial agency in Rokuhara, Kyoto), and for the achievement in the battles, Emperor Godaigo gave him the possession and status of the lord of Koyagyusho district (or Oyagyusho district) in Yamato Province, ever since then, he called himself the Yagyu clan; however, it is said that the articles in "Gyokuei Shui" are nothing but folklore.
実際の柳生氏の事項が明らかになるのは、南北朝時代(日本)の柳生永珍（別名：宗珍、大膳亮柳生永家の子とされる）の頃からで、柳生家の家譜である『玉栄拾遺』によると、元弘3年（1331年）に、南朝(日本)として、六波羅探題の北条仲時・北条時益の軍勢と戦った永珍は戦功によって、後醍醐天皇から賜った大和国小楊生（大楊生とも）庄の領主となり、柳生氏と名乗った事から始まるとされる（ただし、『玉栄拾遺』の記述自体も伝承の域を出ないという）。