A boy who was raised in the Sidonia's underworld, he had troubles adapting after returning to the upper levels. Is a compulsive eater with a large appetite.

A Gauna-human hybrid created by Kunato Developments for fighting against the Gauna, her prowess in combat is rivaled only by Nagate's. She becomes friends with Nagate and Izana.

A Guardian pilot who quickly becomes Nagate's best friend, constantly accompanying Nagate and teaching him about the life inside Sidonia. She is a new third gender of humans who are asexual, yet can change their gender to either male or female depending on the other party.

Initially a Garde pilot in-training with the call number TS-256, Yuhata is promoted to the Commander's aide. She later develops feelings for Nagate and competes with Izana for his attention.

Norio is the heir of Kunato Developments, and also Nagate's fellow Garde pilot assigned to unit 701. He was once the best trainee during the training and the rival of Nagate. But he quit his position after Hoshijiro's death.

Honaka sisters are eleven identical clone sisters who pilot Gardes. En is assigned to unit 703, Ren to unit 706, Ho to unit 705. All of the Honakasisters possess enhanced physical strength and agility. Unlike their looks, they are only about 5 years old.

Kobayashi is the 28th captain of Sidonia who commands the Gardes against the Gauna's attacks. She's myterious, always wearing her mask infront of normal ship crews. She seems cold-blooded who would do anything for Sidonia, but is actually forced to do things by the Immortal Ship Committee.