Prunus Girl
Chapter 42.5Maki-kun goes to look at the results of his high-school entrance exam results and meets a beautiful girl. Could this be a fated encounter? He's thrilled to find out that the same girl, Aikawa Kizuna, not only ends up going to his school, but is in his class. However, he's not so thrilled when he find out that Aikawa isn't a girl! Not a girl, and not really a guy, kind of both--and Maki finds himself getting along with popular Aikawa, getting pulled in to his pace!
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Marugoto Anju Gakuen
Chapter 20Kaguya is a boy in an all-girls' school for demons [fox spirits, succubi, werewolves, etc]. Being the only human is bad enough, but the added risk of his manhood being discovered makes for silly and unbelievable (deliciously enviable) situations.
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Midori no Me
Chapter 1From Aerandria Scans: In a world where people with green eyes are despised and named as bringer of plagues and destruction, Sue seeks a cure for her ailing friend. A holy nun comes into town one day to cure the sick and drive out the plagues. Due to desperation and lack of money, Sue decides to kidnap the nun to plead with her to heal her friend. What she didn’t bargain for what suddenly facing a green-eyed devil!
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Gisou Honey Trap
Chapter 12Keiichirou Mishima is a 15-year-old guy living with his mom until she suddenly decides to fly to Paris to be with Keiichirou's dad. His mom arranges with his uncle Shirasaki to let him stay at his mansion with his two cousins Marie and Tomari, who he met many years before when he stayed with them for a short while. However, Keiichirou has forgotten nearly everything about back then, including why his cousins apparently now hate him.
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Mizuho Ambivalent
Chapter 27From Hells_Castle: Tashiro Mizuho is your typical middle school teen... except for the fact that he is a cross-dresser! When an upper-classman's sister transfers into his class after living abroad, he begins to develop feelings for her and even considers returning to being a male. What awaits Mizuho in the future?
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Boku to Kanojo no XXX
Chapter 54Two teens see how the other half lives! When her mad scientist grandfather accidentally switches their bodies. Akira Uehara is mortified when his best buddy starts hitting on "him," and is embarrassed to look at "himself" in the mirror in her underwear! He can't wait to get back to being a boy. But Nanako Momoi has other ideas--she is starting to enjoy life in Akira's body! From Tokyopop: Rude girl and effeminate boy switch bodies and find that it might be a better fit for both of them. Lots of crazy comedy. Nanako Momoi is the belle of high school... as long as she stays quiet. Once she shows her true self, guys' dreams are shattered for she is a true tomboy. Akira Uehara has the looks and brains, but, unfortunately, his personality is so dull it overcasts a shadow, and nobody notices him. One day, Nanako's grandfather comes up with a crazy invention, and Nanako and Akira trade Bodies! She's him, and he's her!
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Onnanoko Play
Chapter 3Junichi Sasaki joins his school's drama club upon entering high school. However, he soon finds himself dressing up as a girl for his first stage performance.
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Hundred
Chapter 13--- that is the only weapon that can oppose the mysterious life form visiting the earth. The protagonist, Kirasagi Hayato, aims to become a using this Hundred. He managed to get into the battleship university . However --- "I wanted to see you, Hayato!!!" "H-How do you know my name?" Around the roommate, Emil Crossford, who somehow knows him well (?), Hayato gets an uneasy feeling. What's more, just after the entrance ceremony, he gets asked for a duel by the campus' strongest martial arts master Claire Harvey...!? The ultimate academy battle begins here!
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Extrastrous
Chapter 2From BangAQUA: A marvelous actor who has stage fright plays various roles in real life! The agency Catherine is the company which sends so-called extras in real life. Yaegashi Taiga, a marvelous actor that has stage fright, tries his best to fulfill the requests he is given by this company. One day, he is told to work on a request with the newbie Amae Shizuku... But Shizuku has a secret and...?! Please come to our office if anything troubles you! The excellent extras will support you throughout your daily life.
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Nonono
Chapter 0.2A trap named Nono goes to his lesbian friend, Sei, to become cuter than he already is...Note: They're both separate oneshots, but since they're prequel/sequel I just put them together. And traaaaaaaps ;3
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Idol Paradise
Chapter 3From Vampire Knights: TAKAISHI Minori is a cute and perky female fast-food worker who is adored by all the female customers because she looks like a teen idol--a MALE teen idol. Minori is a tomboy and has short hair, so she is often mistaken for a boy. One day after work, Minori spots an unfair fight going on, and leaps into the middle of the fight, ready to even the odds…only to be mortified to learn that she landed right in the middle of a music video shoot for the popular boy band GOLD! She is dazzled by Tomoya, the leader of GOLD. Minori apologizes for her mistake and is about to continue on her way, but not before one of GOLD’s managers sees her and gets a great idea…
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Mr. Clice
Chapter 23Mr. Clice is a story centering on a super dashing spy, the special agent member of Japan's elite espionage program Jin Clice, whose body was mortally wounded by the KGB. The agency had already invested a lot of money in him, so they would not allow him to die so easily. In an act of desperation in order to save his life, the government transferred Jin Clice's mind into a the body of a recently deceased tennis player, which happens to be that of a lovely young beautiful woman! The dashing ladies man has, in essence, gone from being Bond to being the Bond girl!
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Hanayashiki no Juunintachi
Chapter 15From Pink Everlasting Dream Scanlations: Sakura Aki is a penniless high schooler who likes to cook and does other "unmanly" things. His grandfather and father are disciplinary on gender roles and beat up Aki everytime he does a thing that women would usually do, like cleaning. When his father leaves him absolutely broke, and with his grandfather realizing Aki's "unmanly" flaws, he sends him to live at one of the dorms at an all girls' school that he runs, a school where distinguished young ladies of the country attend, the Hanayashiki - Flower Estate-, to teach him a lesson. He meets Kitahiro Renge, a girl with un-ladylike manners and a meat loving obsession. An encounter that's going to save Aki Sakura or just another problem in sight?!
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Megu Miruku
Chapter 15.5Just before they enter high school, the boys Meguru and Shou are whining about the fact that neither of them has a girlfriend. A strange, large-breasted woman shows up, claiming that she will fix their problem, and kisses Meguru. This odd occurrence is pushed out of the boys' minds when they meet up with Souko, a friend from elementary school, who is going to be in their high school. She's grown up into a pretty young girl, and it seems like the boys might have a shot with her! That evening, Meguru realizes that the strange kiss may have had more meaning than he thought: he's turned into a girl! He convinces Shou and his mother of his identity, but no one has any idea how to turn him back. Now he's going to have to learn how to be a girl and let go of his hope of dating his cute childhood friend Souko. What will happen to his hopes for a popular high school life?
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Seikou Gakuen Idol-gumi!
Chapter 6Talentless, shy Tsubasa has just been accepted into the prestigious Seiko Academy. He soon gets mixed up with the most popular kids in school -- and the entertainment world! Forced to join the pop idol group RINX as their lead FEMALE singer, Tsubasa soon finds himself stuck in the middle of a cross-dressing comedy full of mistaken identities, blackmail, and kidnapping!
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Baka to Tesuto to Shoukanjuu
Chapter 30Based on a popular light novel. from Baka-Updates Manga: The protagonist is a guy who is among the stupidest of the stupidest in the school. In this school, your grades can, under the supervision of teachers, take a virtual form to do combat! However, if you leave an examination half way, you get zero marks. A bright and cute girl, Mizuki Himeji, was having a high fever during the examination. Despite her potential to be the second highest scorer in the level, she obtained zero marks for having left due to her illness and is thus allocated to the worst class, class F. Grades mean almost everything. For Class A, they have a smart-looking teacher, a plasma TV as big as the entire wall as their blackboard, personal laptops, personal air-cons, refrigerators, adjustable seats and all kinds of different appliances. Within the refrigerator, there are all kinds of drinks and snacks. Their ceiling is made of glass, the wall lets them put up high-class drawings and plants. As for Class F, the worst class... They have Japanese desks and seat paddings. Their blackboard is dirty and there is no chalk even! Someone complains that the legs of his desk are broken, so the teacher asks, "Didn't we distribute some glue to stick wood together? Glue it back yourself later." Another one complains that wind is blowing in from the broken window. The teacher says, "I got it. I will apply for plastic bags and invisible glue to fix it later." There are spider webs everywhere, not a patch of the wall is clean. A unique moldy smell spreads across the entire room; it must be from the old tatamis used to tile the floor. This is the status of class F. The protagonist feels displeased at such an arrangement, and seeks help from his friends to try to make a change through summoning war!! And they devise all kinds of plans to try to beat the famous class A, intending to get class A's classroom and equipment if they win!!
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Detective Lady
Chapter 114Huang Zixia is an investigative prodigy who proved herself by helping her father solve confounding crimes. After being accused of murdering her whole family due to an arranged marriage, the heroine is on the run. When she meets a prince, they work together to investigate the truth of the murder.
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Koutei Gentei
Chapter 3.2From JShoujo Scans: Mio and Ao are twins and they resemble each other in almost everything, beside the fact that Mio is a girl and Ao is a boy. They get along quite well and they always support each other, so when Ao tells Mio that he wants to become a member of LUNA, a group of young models, she is very excited. But unfortunately Ao can't attend the casting so Mio cuts her hair and decides to impersonate her brother for the casting. Though at the casting they immediately realizes that "Ao" is actually a girl, they decide to let her...
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Kyo->dai dakara nandayo!
Chapter 3From Awakened Memories and Covenant of Darkness: My private tutor, Midorikawa-sensei is a student attending a super elite medical school. He confessed to me and we started dating but I inadvertently lost my virginity! It is because, everyone around me already experienced their first time and I thought it was too late for me. At that time, my non related sister who has always lived separately from me returned. We met for many days and suddenly she is a he. A he who wants to have a romp in the hay with me!?
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NG LIFE
Chapter 51.4Keidai Saeki is a high school student who remembers his past life in Pompeii, living as the Italian warrior Sirix. His friends around him are all also reincarnated - although they don't quite remember things the way he does. Keidai's wife from the past? She's now a middle school boy - while his best male friend is now a cute girl?! Throw in a case of love at first sight, and you have a new look at romance - manga-style!
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Otome No Iroha!
Chapter 5.5Iroha, a masculine girl, and Hifumi, a feminine boy, are siblings who have transferred to a different middle school and moved to their grandparents’ house. However, after the first night much to their surprise they both change bodies, Iroha into a boy and Hifumi into a girl while Iroha tries to get back her girl body how will this turn?
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My Heart Is Beating
Chapter 3017 year old exemplary student Bae Sugu lives alone with his father, the vice principal of his school. Weighed down by his father's expectations, Sugu has to hide his one true passion: swimsuits. He does not know where it comes from, but his passion is pure and genuine - and often misunderstood. But one day, when Sugu is secretly taking pictures of swimsuits by the pool, he is caught by his homeroom teacher who forces him into something ridiculous. Can Sugu find something to get out of the standstill his life has come to? Can his heart beat again? Webtoon from Naver
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Burakon!?
Chapter 6.5A series of unrelated short stories about sisters with brother complexes or vice versa
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