Very little is known about the actual life of Yagyū Mitsuyoshi as the official records of his life are very sparse. Yagyū Jūbei Mitsuyoshi (born "Shichirō") grew up in his family's ancestral lands, Yagyū no Sato, now in Nara. He was the son of Yagyū Tajima no Kami Munenori, master swordsman of the Tokugawa Shoguns, especially Ieyasu and Tokugawa Iemitsu, who prized Munenori as one of his top counselors.
Munenori fought for the first Tokugawa shogun, Tokugawa Ieyasu, at the Battle of Sekigahara, expanding the Shogun's territory. For his efforts, Munenori was made the Shogun's sword instructor and a minor daimyō (provincial ruler), by extending his family hereditary domain up to 10,000 koku. Despite not being the heir of his father as the headmaster of the Yagyū style (and thus far from being an unrivaled swordsman under the Heaven), he received the post for its importance in Japanese politics and Court intrigues, at which Munenori was better than the other members of his clan. Munenori would go on to train three successive Shoguns: Ieyasu, Hidetada, and Iemitsu.
In 1616, Mitsuyoshi became an attendant in the court of the second Tokugawa Shōgun, Tokugawa Hidetada and became a sword instructor for the third Tokugawa Shōgun, Tokugawa Iemitsu, occasionally filling his father's role. Records of Yagyū Jūbei Mitsuyoshi, however, do not appear again until 1631, when Jūbei, by now regarded as the best swordsman from the Yagyū clan, is summarily and inexplicably dismissed by the Shōgun either due to Jūbei's boldness and brashness or his decision to embark on a Warrior's Pilgrimage (武者修行, Musha Shugyō).
His whereabouts are then unknown over the next twelve years—even the Yagyū clan's secret chronicles, which contained lengthy passages on numerous members, has little solid information on Jūbei—until Yagyū Jūbei reappears at the age of 36 at a demonstration of swordsmanship in front of the Shōgun. Following this exhibition, Jūbei was reinstated and serves for a short time as a government-inspector (御所印判, Gosho Inban), taking control over his father's lands until Yagyū Tajima no Kami Munenori's death in 1646.
Jūbei also authored a treatise known as Tsuki mi no Shou (月目之抄) or The Art of Looking at the Moon outlining his school of swordsmanship as well as teachings influenced by the monk Takuan Sōhō who was a friend of his father's. In this work he briefly provides hints on his whereabouts during his absence from Edo Castle from 1631 to 1643 – traveling the countryside in perfecting his skills.
After residing in Edo for several years after his father's death, Jūbei left his government duties and returned to his home village where he died in early 1650 under uncertain circumstances. Some accounts say he died of a heart attack; others say he died while falcon hunting; some during fishing, while still others presume he was assassinated by his half-brother Yagyū Tomonori's attendants.
Jūbei was laid to rest in a small village called Ohkawahara Mura nearby his birthplace, which was also the resting grounds for Tomonori. In keeping with tradition, Yagyū Jūbei was buried alongside his grandfather, Yagyū Munetoshi, and was survived by two daughters and his brother and successor Yagyū Munefuyu. Jūbei was given the Buddhist posthumous name of Sohgo.
Legend has it that Yagyū Jūbei had the use of only one eye; most legends state that he lost it in a sword sparring session where his father, Yagyū Munenori, struck him accidentally. However, portraits from Jubei's time portray him as having both eyes. Several authors of late have chosen to portray Jūbei as having both eyes, though the classical "eyepatch" look remains standard. Others have chosen to have Jūbei lose an eye as an adult in order to incorporate the eyepatch legend.
Due to Yagyū Jūbei's frequent disappearances and the fact of little existing records of his whereabouts, his life has bred speculation and interest and has been romanticized in popular fiction.
In popular culture, Jūbei's eye patch is usually a sword guard with leather wrapped through it. An alternate dramatization to this is found in the manga Samurai Legend, in which a swordsman is seen walking with a sword guard on his right eye, matching the popular culture image, while another character of similar stature follows behind. A group of samurai assume the eye-patched man is Yagyū. The target is disarmed, only for the two-eyed Yagyū Jūbei following behind to reveal himself a second later.
Yet another variation can be found in the anime Shura no Toki. In this version Jubei was initially known as having only one eye, but actually covered the other to challenge himself. However, upon taking the eyepatch off to duel the fictional Mutsu Takato, Jubei actually loses his eye.
Jūshirō Konoe played the role of Yagyu Jubei in a series of nine films produced by Toei studios during the early 1960s, as well as a television series. Yagyu Chronicles 1: The Secret Scrolls (Yagyu Bugeicho - 1961), Yagyu Chronicles 2: The Secret Sword (Yagyu Bugeicho: Yoru Zakura Hiken - 1961), Yagyu Chronicles 3: The Valley Of Outlaws (Yagyu Ichiban Shobu Burai no Tani - 1961), Yagyu Chronicles 4: One-Eyed Swordsman (Yagyu Bugeicho Dokugan Itto Ryu - 1962), Yagyu Chronicles 5: Jubei's Redemption (Yagyu Bugeicho: Katame no Jubei - 1963), Yagyu Chronicles 6: The Yagyu Scroll (Yagyu Bugeicho: Katame Suigetsu no Ken - 1963), Yagyu Chronicles 7: The Cloud Of Disorder (Yagyu Bugeicho: Kengo Midare Gumo - 1963), Yagyu Chronicles 8: The One-Eyed Ninja (Yagyu Bugeicho: Katame no Ninja - 1963), Yagyu Chronicles 9: Assassin's Sword (Yagyu Bugeicho: Katame no Ninja - 1963).
Hiroki Matsukata, son of Jushiro Konoe, fills the roll of Yagyu Jubei in the recently televised film Yagyu Jubei - The Fate of the World (Yagyu Jubei Yonaoshi Tabi - 2015).
Sonny Chiba played a version of Yagyū Jūbei in two films by Kinji Fukasaku - Shogun's Samurai (aka The Yagyu Conspiracy) (1978) and Samurai Reincarnation (1981) - and in the TV series Yagyū Ichizoku no Inbô (The Yagyu Conspiracy) (1978–79), Yagyu Abaretabi (1980-81) and Yagyu Jubei Abaretabi (1982–83). Both films and the Yagyu Conspiracy TV series deal with the role of the Yagyū in the newly established Shogunate. In Shogun's Samurai, Jubei is struck in the eye with a sword. In The Yagyu Conspiracy Jubei is hit in the left eye by an arrow. And in Samurai Reincarnation, he loses the left eye in a practice duel with his father.
Sonny Chiba also portrayed Jubei in the 2004-2005 film series Sarutobi Sasuke Yami no Gundan (Sarutobi Sasuke and the Army Of Darkness).
Yagyū Jūbei was portrayed by Hiroaki Murakami in the 1993 TV series Tokugawa bugei-chô: Yagyû san-dai no ken (Three Generations of the Yagyu Sword), the 2005 TV series Yagyu Jubei Shichiban Shobu (Legendary Swordfights of Yagyu Jubei) and the 2007 TV mini-series Yagyû jûbei nanaban shôbu saigo no tatakai.
Yagyū Kyūbei from the manga Gin Tama takes her name from him, and also wears an eyepatch.
Jubei also appeared in the manga-anime Yaiba as one of the hero's resurrected allies.
Another one is Jubei-chan: The Ninja Girl where a modern high school girl becomes an unwilling heir to the Yagyu Jubei school of swordsmanship.
In Yagyuu Hijouken Samon by Ryu Keiichiro and Tabata Yoshiaki, Jubei is said to have lost his eye in a fight with Yagyuu Samon, his younger brother. Samon is killed by Jubei in the end.
Arc System Works' BlazBlue video game series features an anthropomorphic cat character named Jubei. He is said to be one of the greatest warriors in the world, and is depicted with a sword guard for an eye patch.
The SNK video game Samurai Shodown features a master swordsman named Yagyu Jubei who wears an eyepatch.
Jubei Yagyu is the main protagonist and playable character in video game Onimusha 2: Samurai's Destiny.