Genderswap
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Karin HATES guys. She can't stand the sight of them, let alone be near them. But after a near death experience she finds herself waking up to a guy she doesn't know, within a guy school and in a guy's body!!?!
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The story focuses on the world of Alice Grounds where it is said that the person who has the brilliance of Alice Royal conquer all.
The great thief of the continent Rizel Raffles appears in the wedding ceremony of King of Swords to steal the ring Princess Viola where he is forced to escape on his second attempt and after several events, the King of Swords and Princess Viola will propose to Rizel be part of the "Numbers"?
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Kouta's school-year is off to a great start; this year he and lovely Ayano are in the same class—and they're sitting next to each other! Here's the problem: whenever Kouta gets excited he passes out—and wakes up in a stuffed toy. (No, not in a costume—he IS the stuffed toy.) It's never the same toy and it always seems to have some sexy girl hugging it close. Then his childhood friend Ako gets involved and Kouta's begins to realize Ako is not a child anymore...
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Shimeru Futaba is a fairly ordinary guy who likes his friend Misaki. Futaba is also a member of the wrestling club. One day during recess, his fellow club members give him an erotic magazine. Futaba decides to look at it in the toilet before class, but he suddenly faints after looking at it. When he wakes up, he looks in the mirror and sees... a blonde girl.

It turns out that when members of the Futaba clan become adults, they acquire the "ability" to change sex when aroused. This is how Futaba starts a new life in high school!
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Amamiya just died. Death by bottle tripping... But he is given one more chance, to live... To live in the body of a girl gone comatose, that is. With his new identity, read on how his mind set is slowly changed from a guy to a girl. One thing's for sure, there is more than one body switching in this manga!
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Kurita Yomi suffers from an unfortunate affliction -- when she sleeps her body can be possessed by others. She benefits in her own way from these experiences though...
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This is the story of a village where a deity is--on the day of the village festival, the deity endows a boy, Mao, with a destiny. That destiny is to live as a girl. In a small village where forests, lakes, fields, fish, insects, and flowers flourish, Mao, his sister, and his friend confront fate.
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Haruhi accidentally changes Kyon into female. The consequences of that are more grave than you think.
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Megumi Amatsuka, a rough and tumble nine-year-old boy, always dreamt of becoming the "manliest man on earth." Upon receiving a book of magic from a sorcerer whom he saved from a group of local thugs, Megumi summons a genie in order to make a wish. But due to a sick twist of fate, the genie turns out to be an evil one, and Megumi winds up being the "womanliest woman on earth"! Six years later... Megumi is the most desirable girl in school, but deep within her hot-mama facade is the same trash-talkin,' punk-stompin' boy.
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A humorous short about a boy who transforms into a girl to save the world.
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This is the story of a boy who one day walks into some strange wood and is saved by a nymphomaniac godess who can not only take over his body (turning it into hers in the process) but can also transform him into a girl.
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It's about a guy named Yuuji, who loves to play rugby. One day he just up and dies, in the middle of a rugby match. His spirit is unable to rest, because his team has never gotten a try. So what does he do? Take over someone else's body to accomplish this goal. But... the body turns out to be a girl's!
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Anyone who interested in the artwork.
This is the same artist as Ro-kyu-bu! & Nusunde Lilith.
A story of a guy who get transported into a different world. His gender has changed to a girl and he is forced to live with Mary. She is a Hakubaku. a yokai who eats dream

The series was discontinued due to the author's health.
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Cutie Honey for the 21st Century.
Seiko Hayami a private detective and her partner Hisashi Hanyu, are tasked with solving the cases that the police can’t handle. What they soon uncover is a seedy underbelly of crime perpetrated by an organization that can turn humans into monsters.
With Seiko being overwhelmed by these outrageous cases will a hero arise to help in her stead?
A warrior of love only heard from stories long ago.

[Source: MangaUpdates]
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Urara would really like to be a normal high school girl, but her mad scientist older sister and mother make this a difficult goal. For their latest experiment, they've fused Urara's neighbor and childhood friend Takaharu into Urara's body. After discovering this, Urara destroyed some of the experimental apparatus in a fit of rage, leaving them stuck with each other for the time being. Takaharu is a high school graduate who sells erotic manga while waiting to retake his college entrance exams. Takaharu takes over Urara's body when she falls asleep or passes out, and, to Urara's embarrassment, has been using it as source material for his manga. Will the two of them be able to deal with sharing a body until Urara's family can put things right?
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While on his way to school to confess his love to classmate Kusanagi Mikuru with a love letter, high school 2nd-year Takatou Iori gets run over by a truck to save a cute elementary schoolgirl.

But he wakes up, revived by a perverted doctor, as a full-fledged female first-grader, and is now in the same class as the girl he saved.
Links:
  • Author's Twitter
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    The Culture Research Club of Yamahoshi Academy. The strange events that befall the five boys and girls there, causing their bodies and souls to be swapped around at random. What can be seen from the viewpoint of the others?
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    A "trouble comedy" about a fujoshi girl who meets a yuri otaku boy.
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    27 year-old Ayukawa Yuuji is a mild-mannered biology researcher with a fiancée. After agreeing to being a test subject for a new drug, a young man breaks into his room and declares, "You're going to have my kid!"

    Yuuji suddenly finds himself the sole target of a lost race that turns into dinosaurs, an extremely scary woman with a Goddess-Complex, the yakuza, a mad scientist and one 17 year-old boy who really, really, really wants to sleep with him.

    Series:
    1. Aragami no Ichizoku (4 volumes)
    2. Daichi no Okite (2 volumes)
    3. Genshi Sairai (10 volumes)
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    My name is Midou Maria. But a year ago, my name was Ichinose Rei. This Ichinose Rei was a special existence. The worker force for Ichinose Group’s enterprise comprise of nearly half of the corporate town, Segawa. So Rei was that Ichinose family’s heir.

    But that brilliant future was abruptly snatched away. Given a new name, gender and three hundred million, Rei was banished from Ichinose. Even though he or she, desires revenge, but what can he do all alone? With death as his resolution, Maria roamed around the streets, only to land him in a ruin. In there, there is a community… It’s the secret base for juveniles!

    Together with Yuuki Azusa and Tobe Yuuna, this is the start of a story on mutiny!!”
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    Manaka Makoto, a 24-year-old salaryman without a girlfriend, wakes up one morning suddenly changed into a female, and a knockout at that who attracts just about everyone of the opposite sex. And when he learns through a magical being that the only way he’s going to become male again is by getting aroused (as a woman) he tries to find a way back without any success. But when success finally comes and he switches back, he discovers that he will switch back and forth ANY time he gets close to someone sexually, and there are exceptions…
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    In a not-too-distant future, the Earth has been overrun by a horrifying technovirus. Mechanical parasites, mistakenly created in an attempt to advance technology, attach themselves to human spinal cords and turn their hosts into cyborgs.

    Desperate to rid themselves of this technological terror, the remaining human survivors must band together and learn to defend themselves against their android enemies.
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    Youta and Hikaru, a twin pair of siblings, have grown up together and been close all their life. Since their parents are gone from dusk til dawn running a bar, Youta has stepped into the role of housewife of the family, cooking, cleaning, and generally getting things done. His twin sister Hikaru has always had trouble showing emotion, thereby leading to people misunderstanding her and showing fear of her. One morning after certain things come to light about their family, Youta and Hikaru are involved in a car accident. Upon awakening, they find they've switched bodies!
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    A scientist finds a brain in an alley and implants it into the body of his beloved, Nina. It turns out the brain belonged to a boy, Misumi Yutaka, and he is none too happy to find himself in a female body. What happened to Yutaka's body and why was his brain in the middle of an alley? What will happen to "Nina" when the female parts of "her" body start to have an effect on "his" mind? You'll have to read to find out.
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    Average young girl Kazuki Suou lived a peaceful life with older brother Masaki. That is, until she met Shirou Kusanagi, a boy with secret knowledge of her past, and the dark contract Kazuki was a part of in a former life.
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    Yazaki Yuuri, a transfer student, just wants to avoid trouble in high school. Also, despite how nerdy he knows it is, he's secretly working on writing a light novel. When strange things start happening around campus, an eccentric female student, Sakurabi Yukimi, explains to him that he has the power to unintentionally cause the creatures of his imagination to take physical form! Is it even possible for him to maintain his normal image while he's fighting the imaginary monsters from his formerly secret magic-girl light novel?
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    Yukari, at the tender age of 17, is a renown Edo period novelist who claims visions of Yoshihara during the Edo period gush from his heart. After meeting Mahoro, a girl he swears he knows and has met before, Yukari finds himself falling asleep and waking up in the Edo period as an Oiran. The past and present collide in this time traveling romance.
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    As punishment for slacking on the job, the Shinigami Lapan is ordered to go to the Human Realm in the body of a skeleton to retrieve a wandering soul. However, much to Lapan's lecherous delight, a slip-up lands his soul in the body of the young Alice, a buxom student at a local all-girls school. With the skirt-chasing Shinigami (as Alice) leaving a storm of sexual harassment allegations in his wake, whatever is poor, beskeletoned Alice to do?!
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    Ordinary Kenichi meets an ordinary woman named Hime, they date and get married. But it turns out his wife has a big secret and when tries to surprise her on their first year anniversary with a new puppy, things take a turn for the bizarre! Why is Hime suddenly a guy!?
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    One day, ordinary junior high-schooler Shirahime Kanata is forced by his mother, Konata to sign a contract that transforms him into a "magic girl" in times of trouble. As a magical girl herself, Konata wants to pass her job onto her son so he can protect the peace while she goes on vacation. Unfortunately for Kanata, canceling the contract means he'll permanently change into a girl, so now he's stuck doing an embarassing job. Along with the help of his supervisor, a perverted cat named Moel, Kanata will fight against the "Noise," magical enemies who try to disturb the peace... all while wearing a cute skirt!
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    Houdzuki Maika is a high school girl who, in a sense, is never alone. Her twin brother Maito, who could not survive birth, lives inside of her and shares her body. They switch between who gets to live each day and they share most of their memories. However, the only times they get to see and talk to each other is when they are both asleep, where they share the same dream. Perhaps as a result of this supernatural existence, they are able to see ghosts. There will surely be many mysterious incidents ahead for these twins to face!
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    Iroha, 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've switched genders. The two are left feeling "delighted"...
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    Pu Reum Han led a normal high school life, that is until, he dreams of a lady, looking for his help to find her missing baby. But what if that baby is inside him?

    Original Webtoon:
    http://comic.naver.com/webtoon/list.nhn?titleId=644182&no=12&weekday=
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    Jun and Kaoru are childhood friends with a secret everyone knows about... New series from the author of Kanojo wa Rokurokubi. Released in rough drafts via Pixiv, now serialized in Bessatsu Shounen Magazine.

    Edit: Although the series got serialised he is still sharing his drafts once in a while and currently (June '19) only one out of 6 has been scanlated. This series is not completed in japanese nor here.
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    Sagara becomes a girl in his third year of middle school, and has to deal with his crush on Kurokawa, a female classmate.
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    Back Story: There once was a big war and when the war was over, it was evident that it had taken it's toll on mankind.
    Civilization and society regressed into a barbaric state of self-struggle and hedonism. To make sure that mankind would not repeat the same mistakes, they created a new set of paradigm(laws/rules/rituals), to ensure that the events would never repeat. In an effort to stop the barbarianism, Buddhist ideals such as "finding inner peace within the mind" and meditation became immensely popular. As a result, martial arts quickly grew in popularity in this new day and age. In this new hierarchy, the more powerful you were, the higher your rank was in society. The path of the martial arts quickly became an honorable and reputable way to live.
    And soon after, the age of the martial arts arrived, and flourished.

    Synopsis:
    After foreign assassins killed the Dalai Lama, an attempt was made to find his reincarnation. After 20 years without being able to find the Dalai Lama's reincarnation, the oracle foresaw a location during his meditation. This location turned out to be "Moo Hyuk" High School, a high school where the worlds elite were created. Knowing this knowledge, the below par troublemaker monk, Dang because of a mix up was assigned to the crucial task of finding the reincarnated Dalai Lama. However, known to no one except his instructors, the troublemaker Dang possess a hidden ability and this ability is only shown when he is sexually aroused making his chi explode, turning him into a powerful monster! Not knowing this because he had never been sexually aroused during his training as a monk and unbeknownst to him, his instructor tells him that he should stay away from bottled coke shaped women. He is also put in a special class meant for the "Trash" and the weak, filled with a bunch of weirdo classmates. Will he be able to accomplish the difficult task of finding the reincarnated Dalai Lama with all of these "coke bottle shaped" women around?
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    In the near future, a BCI controller that reads your brain signals and makes your conscious dive into the virtual world of the Internet has become extremely popular. Katsuro, who was arrested for a certain crime, was adopted by police officer Yumeji and serves his prison term while living with his sister-in-law, Rin. However, at the request of his adoptive father, Katsuro investigates Internet crimes in exchange for reduction of his punishment.
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    The clever Bild, who has figured out that it's Al's spirit currently inside Saylie's body, begins a plot to get rid of Saylie, who will become an obvious obstacle in the future...
    Meanwhile, Debroyl asks for Saylie's hand in marriage, claiming that he loves her just the way she is, however...?!
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    Like most teenagers, Mashiro Ichijo has a secret. But Mashiro’s secret is that he’s neither fully male nor female! So far, Mashiro’s been able to live his life as a boy, but all this changes when he’s informed of a new class he must take in order to graduate from his elite prep school. To pass, he must find the “Key”…and the only way to find it is to enter into a nightmare world where his body and soul are put at the mercy of the worst kind of enemies: his classmates!

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