Mikamachi Misao

Misao is a fairly skilled ninja from the Oniwabanshū clan of onmitsu (ninja) previously based in Edo. Misao is the granddaughter of the former okashira of the Oniwabanshū. She was in the care of the last leader of the Oniwabanashu Shinomori Aoshi until Aoshi, Han'nya, Shikijō, Beshimi, and Hyottoko left her to Kashiwazaki Nenji, also known as Okina of the Oniwabanashu, when she was eight. She and Okina had a strong bond, though in Misao's mind, Aoshi remained the best. She also had a special affection for Han'nya, who was always the one to take care of her and taught her how to fight. When she heard that Aoshi was in Tokyo, she went to search for him and runs into Himura Kenshin on the way back to Kyoto.Her weapons of choice are the kunai. Misao is about sixteen years old when she is first introduced, though she appears younger.

Saito Hajime

A former captain in the loyalist Shinsengumi, Saitō has had a long time rivalry with Himura Kenshin, a former manslayer of the Imperialist cause. As a result of his involvement in the Ikedaya Affair, he and his Shinsengumi comrades successfully prevented the burning of Kyoto by an extremist faction of the Ishin Shishi. Nevertheless, the pro-shogunate forces were ultimately defeated and he was forced to go into hiding.
Saitō mastered several techniques of the "Shinsengumi-Kenjutsu." The "Hirazuki" (left-handed stab) technique that Saitō's Gatotsu resembles is based on the real fighting style of the Shinsengumi. Although the Gatotsu is the only technique that Saitō performs, he has been able to perform the same technique in different stances.Besides his overwhelming ability with a sword, Saitō is extremely well-versed in hand-to-hand combat. His fighting style most resembles Boxing as he possesses amazing footwork, defense, and tremendous speed and power.

Takani Megumi

Megumi was born in December 1857 during the Bakumatsu period of Japan. That would make her twenty-two years old during the start of the anime. Like the rest of her family, she is adept at "rangaku" (Literally "Dutch learning") medicine, although she mixes this Western learning with Eastern medicine as well. The fact that Megumi bore the last name 'Takani' spoke of her family's higher class level - peasants during that time were forbidden to carry family names. Megumi was portrayed both in the anime and in the manga as having long, dark hair and dark eyes. In the anime particularly, she usually wore a blue haori worn over a lavender kimono.

Sometimes, Megumi appears to have fox ears popping out of her head, an allusion to her nickname kitsune, which means "fox". Sanosuke especially likes to call her kitsune-onna meaning Fox Lady, though Yahiko and Kaoru sometimes call her this as well. The nickname actually has two meanings: 'Fox' to describe Megumi's wily ways and 'fox' as in a compliment - "foxy lady" or beautiful woman.Like Kaoru, Megumi is a strong-willed woman, but she is also depicted as a more mature and cunning compared to the younger Kaoru.

Hiko Seijuro

Hiko Seijūrō is Himura Kenshin's master.The thirteenth successor to the sword art of HitenMitsurugi-Ryū, Hiko Seijūrō saved young Shinta from marauding bandits who killed his companions. Hiko then took care of Shinta, and renamed him Kenshin ("Heart of Sword") after claiming that Shinta was not a good name for a swordsman.Hiko then trained Kenshin in HitenMitsurugi-Ryū for the next six years.

He became angry and disappointed with Kenshin, because he ran away to join the rebellion against the Tokugawa regime at age 14, knowing that although Kenshin displays extraordinary skill in swordsmanship, he was not prepared in mind and spirit for dealing with the conflicts of the outside world. Hiko isolates himself from the rest of the world, reasoning that he does not have to deal with the ills of society by living as a hermit/potter in a forest near Kyoto.

Shinomori Aoshi

Shinomori Aoshi was raised a ninja of the Oniwabanshou, who worked for the Shogunate government during the Edo period. He helped to raise Makimachi Misao from childhood as a member of the Oniwabanshou. At the suggestion of Kashiwazaki Nenji (better known as Okina), Shinomori was given the position of Okashira at the age of fifteen, in time for the Oniwabanshou to defend Edo Castle.

Aoshi's Subordinates included Beshimi, who specialized in darts and poison, Hyotoko, whose name literally means "Fire Man" and uses flint-and-steel teeth to breathe fire. Also were Han'nya, a skilled martial artist and deft ninjutsu practitioner (also his unofficial second in command), and Shikijo, a "muscle man".
His comrades were
Hanya
Beshimi
Hyottoko
Shikijo

Shishio Makoto

Shishio is extremely ruthless and coldblooded. Living by the belief that weak only exist for the benefit of the strong, he generally appears heartless, though in reality he isn't. For all of his ruthless nature, he was still in love with Yumi, and understood her feelings. He was also able to form some bonds to a degree with Sōjirō and Hōji.Shishio displays very high intelligence, in some ways giving him something of an evil genius persona. He is extremely crafty, being able to hide from the Meiji government despite their efforts to find him, and his plans nearly succeed in bringing them down.

He also learns from his mistakes; after his brush with death from being knocked out with a bullet to the head, he takes to wearing a hachigane (iron headband) to keep that weakness from being exploited.Shishio's sword, like Kenshin's, is a work by master swordsmith Arai Shakku: a blade called Mugenjin lit. "Unlimited Blade",its self-sharpening serrated edge flaked away in a regular pattern as it was used and it had become soaked in the flesh and body fat of the victims he had killed over the years. As a result he is able to execute fire-oriented techniques using the oils as fuel.Shishio's monstrous strength, stamina, resistance to injury, and ability to read his opponent place him in at least the same league as Kenshin.

However, for all of his power and skill, Shishio had a fatal weakness: Because he was set on fire, most of his sweat glands were burned. Therefore,once he engaged in battle, his body heat rose far above normal levels.He then headed the "Juppongatana".The Juppongatana (Ten Swords) is an elite group of swordsmen (mostly) that acts as a special attack force. They fight under Shishio Makoto against the Meiji government.

Its members are

Seta Sōjirō
Uonuma Usui
Yūkyūzan Anji
Sadojima Hōji
Sawagejō Chō
Honjō Kamatari
Kariwa Henya
Iwanbō
Saizuchi
Fuji