Boku no Futatsu no Tsubasa is the story of the self-discovery of a teenager named Makoto who, as a hermaphrodite, has more things to discover than most teens. The focus is on Makoto's exploration of her sexuality, but the manga also shows the development of the main characters' emotional bonding and developing relationships.
- Makoto Kashiwagi
- Makoto was raised by her grandfather as a boy because she possessed male genitalia. However, with the onset of puberty, Makoto also started to develop breasts and so learned that she is a fertile and fully functional hermaphrodite. At the start of the manga, Makoto looks, when fully clothed, like a tall, beautiful girl, and she has adopted female mannerisms—although she continues to use boku for "I", which is usually used only by boys and young men (see Gender differences in spoken Japanese). Makoto is unusually strong and athletic, but somewhat naive because of her sheltered upbringing. She is caught unaware when she first develops physical attraction to other people, and her attempts to deal with her sexuality is played for both humor and drama. She initiates romantic/sexual relationships with four individuals over the course of the story, but in the end seems to realise that her true attraction is to Hiromi. At the very end of the story, it is implied that the two will be in a relationship with each other.
- Near the end of the manga, Makoto learns that she is half-alien. When an alien research spacecraft visited Earth, her mother had a relationship with one of the researchers—a member of a humanoid race which is naturally hermaphroditic. All Makoto's unusual characteristics can apparently be traced back to her "sire".
- Hiromi Ishimaru
- Hiromi is, officially, Makoto's cousin. After her father died, she was adopted by her mother, the daughter of Makoto's grandfather, meaning that she and Makoto are actually not related by blood. Hiromi and Makoto knew each as young children, when Makoto was believed to be a boy, causing Hiromi some surprise when she meets Makoto as a teenager. After Makoto reveals her secret, Hiromi becomes Makoto's protector and tutor. She tries to protect Makoto's secret and steer her away from harm, but inevitably gets caught up in Makoto's entanglements. At the very end of the story, it seems that Hiromi has developed and realised romantic feelings for Makoto, the implication being that they will be in a relationship from there on in.
- Kanna Morisato
- Kanna is a student at the same school that Makoto and Hiromi attend; her older sister is a teacher there. A lesbian by orientation, she unrelentingly pursues Makoto, initially to Makoto's distress and reaping only rejection, while providing some comedy to the story. By her own account, she has had sexual relationships - or at least, sexual episodes - with many girls and she is quite aggressive in her pursuit of partners. She used to be in a relationship with Tamami Komatsu, but now apparently sees her only as a friend. Ironically, it seems Kanna is as annoyed with Tamami's attempts to rekindle their relationship as Makoto initially is with Kanna's advances. In the latter volumes of the series, an emotionally unstable Makoto does initiate a sexual relationship with Kanna, initially surprising the latter with the unique aspects of her physiology. Kanna adapts rather quickly, however. Unfortunately, their relationship appears to be mostly a physical one from Makoto's side of the equation.
- Tamami Komatsu (Komatsu Tamami)
- Tamami is a student at the same school as Makoto and Hiromi. A lesbian by orientation, she used to be in a relationship with Kanna. Although Kanna has moved on and seems to consider her only a friend now, Tamami is insistent that they should get back together. She becomes extremely jealous when Kanna starts to pursue Makoto. When overhearing a private conversation between Makoto and Hiromi, she latches onto the idea that Makoto is a crossdresser or even a transsexual, using female appearance to get close to girls and take advantage of them. She attempts to expose as such Makoto several times, to no avail.
- Ayame Takaishi
- Ayame is a first-year student at the same school that Hiromi and Makoto attend. She is small, cute and innocent to the point of obliviousness; she apparently has trouble understanding what kind of things should be kept secret and, without malice, reveals Makoto's hermaphroditism near the end of the story. Before that, she unintentionally saves Makoto from Kanna by walking in on them in the school's p.e. equipment shed. For a time, Makoto latches onto Ayame, attempting to romance her and make Ayame her new (second) lover, but her advances end up frightening Ayame instead. After this episode, Makoto latches onto Kanna. Near the end of the manga, Ayame is apparently going out with Kohei Hisamatsu.
- Kohei Hisamatsu
- Kohei is a senior student at the same school that Hiromi and Makoto attend. His younger brother attends the same school. Handsome and kind-natured, he impresses Makoto to the point that she falls in love with him, and reciprocates her feelings. After some misadventures and dithering, Makoto dates him for a while and reveals her dual nature to him. Although he initially seems to be able to cope with the situation, Kohei falters during their first sexual assignation. He continues to keep Makoto's secret and maintains a friendship with her, but does move on to another relationship, notable with junior Ayame Takaishi. Incongruously enough, the kind-natured and sincere Kohei is friends with the lecherous Keigo.
- Keigo Moriuchi
- Tomoki Hisamatsu
- Kanako Ishimaru