Garde ace from the 628th training class and sole pilot of the “Tsugumori,” he was assigned to unit TS-028 while training and later to 704. Nagate was raised by his grandfather Hiroki below decks on the Sidonia and has little knowledge of life on the surface and generally keeps to himself. After Hiroki’s passing, Nagate was arrested while trying to sneak into a residential area and steal rice. The ship’s captain then made arrangements for him to be trained as a Garde pilot. He is unable to sustain on photosynthesis like other passengers on the Sidonia and must eat solid food daily.

Tsumugi is a living bio weapon created by combining Gauna organic material with a human embryo. As many aboard the Sidonia did not accept her at first, she observed them by extending her worm-like appendages through the many ducts of the ship with some assistance from Nagate and Izana. As her notoriety grew, however, she was welcomed by the passengers with open arms.

Guardian pilot from the 628th training class, Izana pilots unit 723. “She” is in fact binary, neither male nor female and her appearance reflects it. Izana became Nagate’s first friend upon reaching the surface. While very friendly toward him, she often becomes jealous of Tsumugi and Yuhata.

Yuhata is a late addition to the 628th training class and the younger sister of Izumo Midorikawa, a member of Sidonia’s strongest team, the Akai Squad. She enjoys building model Guardians in her spare time.

He is a Guardian pilot belonging to the 628th training class and is assigned to unit 701. Extremely skilled, he boasted the highest ratings of the class. Norio is destined to inherit Kunato Developments as its 8th president, and has the pride to match his elite standing. Labeling Nagate and Izana as “bad seeds,” he refuses to accept Nagate as the rightful pilot of the heroic Tsugimori.

She serves to Norio and take care of him all the time. She as well as Norio got her body taken over and is forced to follow Scinetist Ochiai's order.

Members of the 628th training class, En is assigned to unit 703, Ren to 706, and Hou to 705. The Honoka Sisters are actually 11 identical clone siblings who underwent accelerated growth and compressed mental training. While they differ very little in appearance and intelligence from their trainee counterparts, the Honoka Sisters are a mere five years old.

Kobayashi is the 28th captain of the Sidonia as well as its commander. She wears a full-face mask resembling those worn in Noh theater while in the presence of the crew. Ever level-headed, Kobayashi is willing to make tremendous sacrifices to ensure the Sidonia’s survival. However, she enjoys mingling with the passengers in various disguises.