Otome is a girl who is half. During high school, she encounters an animal-loving and mildly mysterious Natsume-sensei. She is also struggling with her social relationships. With this encounter, will her school life change?

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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In the Otome no Omocha series:

Vol.1 - Otome no Omocha

Vol.2 - Zoku Otome no Omocha

Vol.3 - Otome no Omocha Sweet

Story One: Otome no Sainou

Nakanishi Kiyoshin, nickname Onii-chan, is a 14-year-old, chivalrous heroine. She witnesses a guy, Kashiwaki Sachikana, being confessed to by another guy. The confessor gets aggressive, and Nakanishi steps in. After that, Nakanishi and Kashi-kun become friends, and then...

Story Two: Tsuki Iro Secret

Back in elementary school, Alice ("president" & "me" in the manga) met a boy who helped her out. Now president of her middle school, Alice meets a magical sorcerer named Lu ("mage" in the manga) who can't go back until the next full moon. All the students in her school dislike her and think that she is not good enough for the presidency. Where is the boy who helped her out?

The everyday lives, games and hijinks of high-school girls at an all-girls school.

An aspiring manga artist joins her new high school's manga club, and decides to revamp it after learning they don't actually do much.

Miharu, a recently enrolled student at the Seven Saints Girls Academy, is kissed on the cheek in greeting by her friend Sara. Little did she know that Sara's cousin Itsuki saw the kiss and develops plans for poor little Miharu...

From Tsundere Translations:

Ogdoas Private Academy...
Under the new, young headmistress, freedom, independence and self-fulfillment are the motto of this mission school. However, among the nuns there those who are concerned about order and morals within the school and who oppose the head-mistress's ideas.
And without anyone knowing, right now, at this school... a battle between good and evil is about to take place!

A continuation to Shion and Nashida-sensei's story called "Teacher's Pet" can be found in Yuri Hime Wildrose volume 2

From MangaHelpers:
The story begins in 1420, right as what would be known as the Bohemian War began. A young girl named Sharka is raped and left for dead among the corpses of her whole town, but she manages to survive. She is picked up by the Bohemian forces, who put a gun in her hands and take her on board as a soldier. Will Sharka be able to fight and take her vengeance?

From Chibi Manga:

You have been chosen to be my 'princess' --- always unlucky, high-school student, Natsuno Youko. a naked guy...dropped in front of her!!! Io came to earth to search for the most tuned in Hako to bear his child ...!?

Mizuho can't believe his ears when Grandpa's will is read out. Grandpa's final wish is for Mizuho to attend the same academy as Mizuho's mother. The catch is it's an all-girls school. With the help of his friend Mariya however, he gets a makeover good enough to fool everyone at the academy.

A direct sequel/side story to Himitsu no Kaidan.

Chihaya is a boy that is looked down because he looks like a girl. Due to that reasons, he isolates himself at home. His mom suggests that he should go to Seiou Academy which is an all girls school. Thus, the story started...

From Kawaii Scans: She is your stereotypical airhead school girl, with one exception, she has amnesia. She recently transferred into a new school where things work different, mainly magic. She is Mochiduki Tsubomi, and she doesn’t remember anything before she transferred. Enter yet another transfer student – the beautiful yet arrogant bishojo, Izayoi Yukiji. She’s after Tsubomi, but why? What does Yukiji want? What mystery does Tsubomi hold?

It's the Meiji Era in a slightly alternate Japan, and the Gregorian calendar has just come into effect. The fox-eared girls living in the youkai part of town are about to be put to work together with a delegation of young human soldiers, to promote interracial understanding. So what will happen when Zakuro's strong personality collides with human sensibilities?

From Ochibichan:

Ibuki Noa is an eighteen-year-old girl who has never had any experience with love. In order to maintain the family's inn, her mother then made her go to Oofujiya Inn to carry out a secret plan to find a spouse! To only just experience her first love, how would the spouse scout go?

Sixteen-year-old Nene Kashiwagi has undergone a transformation from a sporty girl to a chic one--or, at least, she's trying to become chic so that she can finally find love! Her efforts only gain her teasing from her (former) friend, Jun Endou. But when Nene's first attempt at finding love goes awry, Jun steps in to rescue her in the most unexpected way.

For the sake of his little sister, a boy tries his best at becoming a star gravure idol.

Two radio hosts finish their second show and are getting ready to head home. However, one has a different idea...

From Serenus-Dreamers:
Asuka is a guy who has likings for girly things like shoujo manga, baking, and sewing. However, his mother forbids this and wants him to grow up manly. He starts learning kendo and karate and grows up to be the stoic guy his mother wants him to be.
But can he fight the urge of falling in love and revealing his true self?