In the reorganization of the ranks in late 1864, he was first assigned as the fourth unit's captain. At Nishi Hongan-ji in April 1865 he was assigned as the third unit's captain. Saitō was considered to be on the same level of swordsmanship as the first troop captain Okita Sōji and the second troop captain Nagakura Shinpachi. In fact, it is rumoured that Okita feared his swordskill. Together with the rest of the Shinsengumi, he became a hatamoto in 1867. After the outbreak of the Boshin War (1868–1869), Saitō took part in Shinsengumi's fight during the Battle of Toba-Fushimi and the Battle of Kōshū-Katsunuma, before withdrawing with the Shinsengumi's survivors to the Aizu domain.