If you liked
Princess Principal
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...then you might like
Spy Kyoushitsu
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Both these shows center on a small group of young female spies who want to shape the world better after dealing with trauma that comes with war. Both shows go to great lengths to really establish setup their missions of espionage and go show their execution. Both shows are fairly serious with some light moments of comedic relief and both evoke a period setting, with Princess Principal going for a steampunk turn of the century feel and Spy Room going for a post-World War I look with its setting.
If you liked
Murder Princess
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...then you might like
Tensei Oujo to Tensai Reijou no Mahou Kakumei
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Though differing in their base concepts, Tensei Oujo being an isekai and Murder Princess being a high fantasy, it's not a stretch to compare the two. A blossoming relationship between two girls, subtle or overt, doesn't matter. Both these anime feature girls with contrasting personalities working together for a greater goal and a greater friendship.
If you liked
El Cazador de la Bruja
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...then you might like
Shokei Shoujo no Virgin Road
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El Caz and Virgin Road share a similar premise, an odd couple; the paring of a girl on a mission with her target objective, in El Caz's case, Nadie is intending to make Ellis her bounty and in Virgin Road, Menoue intending to kill Akari. Both shows feature magic and fantasy and strange organizations operating behind the scenes. Both shows have yuri themes. One could probably recommend the entire Girls with Guns trilogy, with NOIR and MADLAX being the other two but of the three, El Cazador is the most similar.
If you liked
Fruits Basket 1st Season
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...then you might like
Taishou Otome Otogibanashi
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Both shows exhibit this same gentle tone of a mix of silly comedic moments but a lot of heart tugging dramatic moments. Both shows feature a main girl with a sunny personality who is able to pull characters from their lowest points in their emotions just by showing she cares. Both shows feature characters from troubled families with an over bearing cold family head, in Fruits Basket you have the Soma family lead by Akito and in Taisho Otome you have Shima family lead by their cold distant father.
If you liked
Taishou Yakyuu Musume.
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...then you might like
Hachigatsu no Cinderella Nine
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Both series are about a group of female students joining together to play baseball. In both shows they also face obstacles in forming their team, in the case of Taisho Baseball Girls, gender norms of the era, in Cinderella Nine opposition by the student council.
If you liked
Animegataris
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...then you might like
Mahou Shoujo Ore
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Animegataris and Magical Girl Ore are satirical parodies of anime. In the case of MGO it's satirizing the magical girl genre of fantasy and shojo tropes while Animegataris parodies the medium in general. Both are comedic parodies of their respective genres and of the mediums.
If you liked
K-On!
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...then you might like
Urara Meirochou
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Both shows are a about a group of young girls that come together starting as strangers then become a close tightknit group of friends with each of their own quirky personalities that contrast and compliment each other.
If you liked
School Days
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...then you might like
Kuzu no Honkai
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Both series feature teenagers overwhelmed with emotions and learning how to grasp relationships while making mistakes along the way. Relationships in both shows grow more complicated with more people entering the focus of the web of relationships.
If you liked
Pita Ten
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...then you might like
Kobayashi-san Chi no Maid Dragon
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Both series have a main characters who live otherwise ordinary lives until a fantastic being comes into their life and craziness unfolds.
If you liked
Scrapped Princess
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...then you might like
Akatsuki no Yona
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The plots do differ but they do share elements, a spoiled Princess surviving in the wild with only a few caring guardians and is the target of everyone, fantasy elements, great animation and music.
If you liked
Shinseiki Evangelion Movie: Air/Magokoro wo, Kimi ni
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...then you might like
Mahou Shoujo Madoka★Magica Movie 3: Hangyaku no Monogatari
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Both films share enough in common. Both are deeply complex and have confusing plot lines that converge to a major climax to twist everything previously established by its predecessor, combined with dazzling visuals in an apocalyptic thriller.
If you liked
Shinrei Tantei Yakumo
|
...then you might like
Dantalian no Shoka
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The two series feature on a male-female relationship in unusual circumstances. Dantalian and Yakumo both are heavy on the supernatural elements and do this in a sort of mystery of the week style.
If you liked
Scrapped Princess
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...then you might like
El Cazador de la Bruja
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Both series are told in a very episodic fashion where the characters are always on the move from one place to the next meeting new characters and having new adventures. Both series also deal with a character is being hunted down and having to escape danger each time from hunters and a large shadowy organization and/or villain.
If you liked
.hack//Sign
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...then you might like
Angel Beats!
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Both series feature some kind of virtual world, Angel Beats takes place in some sort of virtual afterlife and .hack// inside an MMORPG. They both feature a main character who's lost his memories.
If you liked
Batman: Gotham Knight
|
...then you might like
Halo Legends
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Both are anthologies based on some source material and created by various studios and directors.
If you liked
Noir
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...then you might like
Higashi no Eden
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Noir and Eden have the same espionage mysterious amnesiac style characters. While Noir is darker than Eden they have many similarities to each other in plot.
If you liked
Gunslinger Girl
|
...then you might like
Phantom: Requiem for the Phantom
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Gunslinger girl also deals with girls packing heat in a secret organization of assassins.
If you liked
Chrno Crusade
|
...then you might like
Mai-HiME
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Chrono Crusade and Mai both deal with similar themes, an older sister and a younger brother, death, destruction and magic. Both get pretty heavy later in their series but still have their share of comedic elements.
If you liked
Madlax
|
...then you might like
The Third: Aoi Hitomi no Shoujo
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Both involve a main female who is a profession of several jobs.
If you liked
Digimon Adventure
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...then you might like
Monster Farm: Enbanseki no Himitsu
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Another breed of monster show, this along with Pokemon and Monster Rancher was one of the big 3 monster related shows. Filled with crazy creatures and adventures, if you liked this show (or Pokemon) you will very likely enjoy this series.
If you liked
Tsubasa Chronicle
|
...then you might like
Cardcaptor Sakura Movie 2: Fuuin Sareta Card
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Tsubasa Chronicle is the alternate story spin off of Cardcaptor Sakura. You will also find the plots from the second movie and Tsubasa are strangely similar
If you liked
Chrno Crusade
|
...then you might like
Elfen Lied
|
Both are a deep dark horror/thriller animes with a unique blend of characters. Both certainly have their share of fan service and disturbing horror.
If you liked
Sakura Taisen
|
...then you might like
Erementar Gerad
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Both are action Steam Punk Animes with a dash of heavy fantasy.
If you liked
Bakuten Shoot Beyblade
|
...then you might like
B-Legend! Battle B-Daman
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Very similar in the nature of the competition styles and characters. Both are shonen sports animes.
If you liked
Kannazuki no Miko
|
...then you might like
Tatakae!! Iczer-1
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Both are heavily romance and lesbian themed Anime. Kannazuki and Iczer are also mecha and sci-fi anime.
If you liked
.hack//Sign
|
...then you might like
Arc the Lad
|
Both are Bee Train productions and both involve some forms of sword and sorcery.