Witch Hunter
Witch Buster

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Both have similar : - main characters - organisation that protects mankind - foes with unnatural abilities and powers 

Aside from the fact that Tasha Godspell screams Allen Walker, these two shounen series share a similar feel in a sense that both contain a considerable amount of badassery, humor, and an interesting gothic storyline. 

To be honest, the reason why I picked up Witch Hunter was because the main character, Tasha Godspell, reminded me of Allen so much. I later learned that he was in fact designed after him. Witch Hunter, like D.Gray-Man, focuses on an organization that aims to get rid of an evil. The character designs are very similar as are the ideas of unique weaponry for each person. While reading the series, you feel like you are reading another version of D.Gray-Man, only with a greedy, more selfish version of Allen Walker. 

Naive yet fiercely loyal and moral boy is fighting against "evil," yet can't truly bring himself to hate this "evil," as he soon comes to find that there is good and bad no matter which side he is fighting for, and that it all ultimately boils down to the fact that we are all still human. Expect to find good development of side characters, shonen-esque art, classic (though sometimes a bit mary-sue) fights, and struggles to become stronger for one's friends. 

The main character of "Witch Hunter" (Tasha Godspell) is in certain ways similar to the main character of "D.Gray-man" (Allen Walker). Both Allen and Tasha are swindlers and they are whited haired. They both work for a certain organisation, Allen for the "Dark order" (Established in order to hunt down demons) and Tasha for "WH" (Witch Hunters). Allen does not seem to hate the demons so he only tries to free their souls and Tasha, unlike most other witch hunters never kills a witch because he dislikes the idea of murdering them. In later chapters in D.Gray-man it would appear the "Dark order" is using the powers of demons for assistance and the "WH" organisation has some witches working for them from the very first chapters. I can easily say that who ever likes "Witch Hunter" will without a doubt enjoy reading "D.Gray-man" and the other way around. read more 

It's an action/adventure/fantasy/comedy/shounen. If you like theses things all rolled up into one, then I think you may like this. It's your typical shounen, but it's still worth a look at. 

The concept behind Soul Eater and Witch Hunter has a similar theme involving an organization of people with special talents along with their partners. Such, expect some character dynamics and relationships being explored throughout both series. There is action for both series in which the world functions quite different when compared to our own in terms of battles/wars. Rather than having advanced technologies though, their settings plays on a more fantasy theme. Comedy is also present throughout both series accompanied by humorous dialogues in the form of character interactions. 

Both involve the concept of witches, but witch hunter is more of superpower'd humans vs witches while soul eater is shinigamis vs witches. They both have multiple protagonists and show their own perspective in each chapter. Also Death the kid in soul eater resembles Tasha in witch hunter , as they both use guns and have "partners". 

From the surface, both manga doesn't seem too similar. However, both Claymore and Witch Hunter shares many similarities. In fact, both series takes place in a fantasy like setting where technology doesn't seem to be modern but instead gives off that feeling of natural fantasy. Claymore follows more of a dark fantasy like setting though with more violence and gore. Witch Hunter on the other hand keeps up with its more traditional tone. From both series, there's a background involving various battles from factions. Each faction controls their own domain and hopes to gain the upper edge throughout their series. The main female protagonist from both series are also tough. Then, there's the aspect of a race existent in both series that serves as the primary factors that drives the story. The female character also plays more of a dominant role and there's plenty of action delivered throughout the volumes. read more 

Taking place in a fantasy world, Fairy Tail and Witch Hunter uses concept of magic as a prominent theme. The main characters possesses supernatural abilities that enables them to fight their foes. And throughout both series, the main characters encounter dangerous adversaries. There are various guilds/teams in both series with a large cast of characters. Some of the featured arcs/story elements also pits these teams together in battle. Witch Hunter has more of a war-time like atmosphere while Fairy Tail crafts an adventurous story. But despite this, I'd recommend both if you're a fan of fantasy fiction. 

Both are about witches as the clue is in the titles, both mangas are about the struggle for world power or domination between the different groups of witches and how the male protagonists come in to play in all this. Both protagonists harbour great powers which helps to make them the most dangerous/deadliest which is why some witches will support them and others will oppose them.