This is a list of recurring characters and cast in the anime/manga/novel series RahXephon. Characters without speaking parts or who only appear in one episode or chapter are not included. The characters are first described as they appear in the TV series, followed by their portrayals in the other story versions.
At the beginning of the series, Ayato Kamina is a student and artist living with his mother in Tokyo. Most of his artwork shown in the series consists of drawings or paintings of a girl on a cliff looking towards the sea. He has birthmark-like symbols on his belly resembling runes, which are revealed to be a sign of his being a potential instrumentalist for the RahXephon.
After being taken from Tokyo by Haruka and the RahXephon, Ayato moves in with Rikudo Shougo, Haruka's uncle on Nirai Kanai. At first, this arrangement does not sit well with Ayato, as Haruka and her younger sister Megumi live in Rikudo's annex, but they slowly adapt to each other's presences. As a stranger from Tokyo Jupiter, Ayato struggles to find his place and acceptance in the outside world. Although he pilots the RahXephon in defending Nirai Kanai, he questions his abilities and self-worth. He also struggles with trying to piece together and understand his relationship with Haruka, handling the feisty Megumi, and interacting with the other TERRA personnel, who regard him with a broad spectrum of reactions, from acceptance and friendship to cool scientific interest to distrust and even contempt.
It is revealed that Quon is genetic provider of both Ayato and Itsuki Kisaragi while she is sleeping. Conceived with the help of Ernst von Bähbem and raised by Maya as an instrumentalist — someone who can successfully use the RahXephon to re-tune the world. There are several other instrumentalist candidates, but at this point of the series most have passed their ideal age.
At the end of the series, Ayato succeeds in becoming one with the RahXephon, and re-tunes the world. In this new world, the great dimensional split never happened, and Tokyo Jupiter never existed. Ayato is now an adult and married to Haruka and have an infant daughter named Quon.
In the movie, Ayato is Maya's naturally conceived biological son. In this version, he has to remain in his position as a "Watcher of time" and can not return to the world.
In the manga, Ayato is not just the result of in vitro fertilization but also of in vitro growing; multiple tanks with Ayato clones growing inside them are shown.