Differences

Anime: In the anime we only see Goheh. There is no word of Kiheh. Goheh used to be a student at the Kamiya Kasshin dôjô back when Kaoru’s father was still alive and the teacher. Because Goheh wanted to use his sword to kill and not to protect, Kaoru’s father expelled him from the dôjô. Years later, Goheh reunited a gang that attacks the dôjô. Failing in his task because of Kenshin Himura, Goheh hires Sansouké Sagara to kill him. Goheh takes advantage of Kenshin and Sanosuké finghting to attack by surprise but he fails once again.

Manga: Goheh has a brother Kiheh. Kiheh poses as Kaoru’s housekeeper when he is in fact plotting against her to take possession of the dôjô and the land because it has a high financial value. As in the anime, they hire Sanosuké to kill Kenshin when they fail in their mission the first time. But in vain.

Yahiko and Yamagata Switch:

Anime: Yahiko appears in the second episodes of the series. Whereas Yamagata is introduced in episode 3.

Manga: Yahiko appears in episode 3 whereas Yamagata is introduced in episode 2.

Yahiko’s savior:

Anime: Kaoru goes to Yahiko’s rescue from the Shûei gumi and Kenshin comes to assist her.

Manga: Kenshin deals with the Shûei gumi by himself.

Mégumi returns to Kanryû and Sanosuké vs. Shikijô

Anime: Sanosuké tries to stop M2gumi from returning to Kanryû when he meets with her in front of the gate of the Kanryû’s mansion. That’s when Shikijô appears. A fight begins between the two of them. Sanosuké defeats his opponents but Béshimi kidnaps Mégumi.

Manga: Sanosuké is angry at Mégumi for killing his friend with the opium that she sold him. He does not try to stop her. Mégumi returns to Kanryû’s mansion and is once again a prisoner. Sanosuké’s fight actually takes place in the mansion.

Raijûta, Yutarô and the Shinkô Ryû

Yutarô’s comeback:

Anime: Yutarô returns in episode 83. He awaits at the Kamiya dôjô and immediately begins fighting with Yahiko when he arrives. He has come with a German professor, Hans. This lead into a filler arc.

Manga: Yutarô returns only at the end of the manga. We notice his name on the board of the Kamiya Kasshin Ryû under the assistant instructor’s section, along Yahiko’s.

Kyôto Arc
Misao meets with Kaoru and Yahiko:

Anime: when Kenshin leaves the Aoiya, Misao pursues him in Kytôto. At the same time, Yahiko identifies Aoshi in the middle of the crowd. He chases him with Kaoru only to collide head-on with Misao.

Manga: Since Kaoru and Yahiko are staying at the Shirobéko, they must work in order to pay for they sty. Three days after Kenshin departed from the Aoiya, Misao enters the Shirobéko to get something to eat and notices the poster that Kaoru put on the wall saying she is looking for Kenshin.

Whereabouts of Hiko Seijûrô:

Anime: After the incident with Chô, Okina is able to find Kenshin’s master location and tells Kenshin about it before he leaves from the Aoiya.

Manga: Kenshin receives the information of Hiko’s whereabouts by a signal flare, three days after leaving the Aoiya.

Owl’s torture:

Anime: The only member of the Owls that manages to return to Shishio’s hideout base in the Hiei Mountains to report their failure of raiding the Aoiya Inn has boards nailed to his body, as though he has been crucified.

Manga: As the Oniwabanshû don’t manage to get the Owls’ member to talk, he sent back to Shishio’s base with hot candles and large nails that keep them in place, melting on his hands.

Aoshi visits the Aoiya:

Anime: This scene doesn’t appear in the anime series.

Manga: Aoshi returns to the Aoiya after years of absence and after fighting Okina and defeating him. He wants to know about Kenshin so that he can kill him. As no one will help him find Kenshin, Kaoru and Yahiko speak up for the frightened Oniwabanshû members. Aoshi leaves a message for Kenshin saying that he’ll be waiting for him at Shishio’s base.

Hôji’s trust:

Anime: To find out if Hôji’s responsible for failing to burn Kyôto to the ground, Usui directly asks him when meeting up with Shishio and all of the Juppon Gatana. Whn Hôji lies about having anything to do with it, Usui bends back his left index finger.

Manga: Usui ripps off seven of Hôji’s nails (7 is the number of the Juppon Gatana member that would have been betrayed and left behind if the Great Fire of Kyôto had been a success).

Usui’s death:

Anime: Saitô uses his Zéroshiki Gatotsu and pins Usui up against a wall.

Manga: The Zéroshiki Gatotsu tears Usui in half, pinning his body from the stomach up on the wall.

Revenge arc or Jinchû arc

The entire arc doesn’t appear in the anime series. But we get some part of it in the OVAs.