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Naota Nandaba Naota, 12, is the main character. He believes he is normal, living in a normal town, full of crazy people. Unbeknownst to him, he has huge N.O. powers. Every episode he states that nothing ever happens in his town, even after the unexplainable and amazing happens. He carries his brother’s baseball bat with him because he misses his brother. Naota is internally struggling with the recognition of his existence and independence from looking up to his brother, and to himself.
Haruko Haruhara Haruko, 19 (or so she claims), is a pink-haired girl from outer space. She rides a yellow Vespa and wields a left-handed Rickenbacker bass guitar as a bizarre weapon of sorts. She becomes the Nandaba household’s maid and plays on a rival team of the Mabase Martians for extra money. She has also apparently had past relations with Amarao. This mysterious character is the catalyst for FLCL’s entire plot. Her real name is revealed to be Haruha Raharu by Amarao; this may be another alias, however.
Mamimi Samejima Mamimi, 17, believed herself to be Tasuku’s girlfriend, though since he has gone away she dotes on Naota. She attends school infrequently, smokes and has pyromaniacal tendencies, and spends most of her time under a bridge. It is likely that her parents are separated. She has a rather peculiar tendency to name many things after her personal nickname for Tasuku, “Ta-Kun”.
Canti Canti is a robot with a television set for a head. He was manufactured by Medical Mechanica. It is later revealed that Atomsk was contained inside him. Atomsk’s symbol appears on Canti’s screen when he fuses with Naota.
Kamon Nandaba Kamon is Naota’s father, a former pop culture journalist working as a freelance writer. For a while, Haruko tries to use a copy of the father’s body as her plaything, though the corpse of the real father is eventually found and reanimated by Naota.
Shigekuni (Naota's Grandfather) Nandaba Shigekuni is Naota’s grandfather. He owns the family bakery and coaches the local baseball team, the Mabase Martians. Because Mamimi was with Tasuku, he despises her.
Ninamori Ninamori Eri, 12, is Naota’s classmate. She is the daughter of the mayor of Mabase and class president. She is interested in Naota.
Naota's teacher Miyaji Junko is Naota’s eccentric sixth grade teacher. Her students have given her the nickname “Miya-Jun”.
Commander Amarao Commander Amarao works for the secret part of the Foreign Embassy department of the government. This group knows that aliens exist, and try to keep them from the public. Thus, Haruko/Raharu is a big problem for them. Amarao has fake eyebrows made of nori which protect him from N.O. Amarao seems to have had a past relationship with Haruko similar to Naota’s.
Lieutenant Kitsurubami Lieutenant Kitsurubami is an attractive young woman on Amarao’s staff. Amarao makes a pass at her in the final episode, though she resists him.
Naota's brother Nandaba Tasuku, is Naota’s older brother who moved to America to play baseball. Mamimi believes that, since Tasuku saved her from the fire at their old elementary school, he likes her. From context and the fact that he gets another girlfriend in America, it is apparent that Tasuku has no real love for her. Although he never actually appears on screen, he does have some weight in the story.
Atomsk, the Pirate King Atomsk, also known as the “Pirate King”, is the most powerful space pirate in the galaxy. His N.O. is great enough to steal planets, and when he uses his power in episode 6, the ground and items on it are moved by it. He is a bird-like creature, resembling a phoenix. Amarao is portrayed inaccurately imagining Atomsk’s appearance as humanoid when he describes him to Naota. In an interview, the director clarifies that Atomsk’s true form is indeed that of the bird, and Amarao’s mental image was of a man because he believed that Atomsk and Haruko were lovers.

    FLCL box set