The worlds of anime and manga seem to go hand-in-hand, but the stories between them could actually be drastically different. There are many reasons for this. The anime might be intended for a more general audience while the manga was aimed at a niche crowd. The anime might try to avoid controversies concerning the original manga. Don't forget, the manga doesn't always come first; there are actually quite a few times when an anime and manga were produced alongside each other.
This list will take a look at some examples where a series's anime and manga were surprisingly distinct. Spoilers will follow and remember, a popular story might have more than one adaptation, so a lot of these mangas also have a truer-to-the-text adaptation.
10 Fullmetal Alchemist
While Brotherhood adapted the story a bit more directly, the 2003 anime was a different story. Not only were various characters who appeared in the manga cut from the anime and new characters were also developed, such as the antagonistic Dante.
Some of the more villainous characters were rewritten to be more sympathetic, like Selim Bradley, and vice versa, like Basque Grande, who became much more sinister despite being a posthumous character. One change that upset quite a few fans was that the famously short Edward never has a growth spurt as he does in the manga.
9 Shaman King
In the Shaman King anime, where humans can channel powerful spirits, things especially started to change significantly from the manga once the tournament arc started.
The manga has a bittersweet ending where Yoh's evil twin brother Hao becomes the Shaman King, although he seems to give up his plans to destroy humanity, at least for the time being. The anime changes this to have Yoh beat Hao. Generally, the anime tended to be lighter than the manga, with many characters who die in the manga surviving in the anime.
8 Hellsing
For this vampire-themed story, the anime caught up with the manga surprisingly quick, meaning that the series even had to make up its own antagonist: the evil Incognito. Just as Alucard draws from Dracula, Incognito was believed to be influenced by the famous movie vampire, Nosferatu. Similarly, fellow villain, Helena was also created for the anime.
Many characters from the manga were cut as well as the Millennium arc, but some original villains did show up, even if Incognito was now the major threat.
7 Sailor Moon
This popular anime in which a collection of schoolgirls become superheroes in sailor fuku at least has the excuse that, while the manga technically came first, the anime was actually being developed alongside it. A lot of new story arcs, like the characters forgetting they had powers, were added to the anime give the manga more time to be finished. The monster-of-the-day formula was gradually phased out after the early story arcs in the manga, to the point where the fifth story arc did not have one.
Compare this to the anime, where it was such an integral part of the show that a new one, Phages, had to be made up for the last story arc. Characters could also be drastically different between the two mediums. Infamously, towards the end of the run the anime adapted a manga story about Ami falling in love for the first time, forgetting it already gave her a love interest in the first season.
6 Fruits Basket
The first anime, which revolves around a family cursed to become the animals of the Zodiac, partially has the excuse that it wrapped up its story five years before the manga did. However, it generally focused more on comedy than the original manga, such as turning Shigure into the comic relief of the show. Part of this softer approach came from mostly adapting the earlier chapters.
One of the anime's most infamous changes was actually unintentional. The villain Akito is ultimately revealed to be female in the manga but since the anime was being made before the manga chapter that confirmed this was released, the character was presented as biologically male. In addition, Akito goes from refusing to lift the family curse to being unable to lift it, with the curse now shortening his life span.
5 Princess Tutu
Similar to the above, this anime has the perfect excuse to be drastically different from its manga. It not only came out first, but the manga was also released a few days before the anime actually ended.
The anime boasted a much larger cast, famously including humanoid animals, which disappeared in the manga, with the exception of Mr. Cat, the schoolteacher. Probably one of the most famous differences is that the heroine Ahiru is actually a duck turned human, albeit a magical girl in the anime, and ultimately has to remain a duck by the end of the story, but is just a human girl in the manga. A supportive character, a living puppet named Edel, was also notably changed to be the villain of the manga.
4 Pokémon
There are technically multiple Pokémon mangas, but the most famous is probably Pokémon Adventures, but there are many differences between it and the famous anime.
Satoshi (better known as "Ash" in the English dub) might be the main character in the anime, but Red, the character from the video games, is the main character here, appearing with Blue, Green, and Yellow. Technically, it could be argued that Red and Ash essentially were the same character at this point in the franchise, but different incarnations seem to have diverged on that. Storylines also tend to be more violent and darker compared to the anime, like some of the gym leaders doubling as members of Team Rocket.
3 Magic Knight Rayearth
In this classic anime series, where three girls are transported to another world where they become magical warriors, often went in different directions from the manga.
Generally, the anime tended to be more action-oriented than the manga with new battles being added to the story. One of the villains, Alcyone, is given a redemption arc and a different death. Many characters were also killed off in the anime only to turn out to be more important later in the manga's story, causing the story to be changed in various ways. For example, one such character who was killed off in the anime, Presea, had to be replaced with a twin sister who pretends to be her, Sierra, a new character.
2 Ultra Maniac
In this manga, a young girl befriends a young witch from a magical world who is trying to improve her magic. As an homage to classic magical girl anime, the animated version changed the plot to be about young witches competing to become queen, specifically searching for magical stones so that one of them will marry their world's prince. Because of this subplot, a villain, the heroine's friend-turned-rival, was added to the story.
Allegedly, there was an interest in turning the manga into an anime before it was published, which might explain the difference in storylines.
1 Devilman
While a lot of people were introduced to the series through DEVILMAN crybaby, it was not the first anime, which drastically changed the main character's origin. The original main character, Akira, actually dies at the start and a demon takes over his body as opposed to having him merge with a demon. After he falls in love with Miki other demons plot to destroy him.
The series adds a bit more comic relief like the character of Lala, cut out Satan, and even keeps Miki alive at the end of the series, although it's implied that the characters' adventures are far from over.