Since he grew up living with his grandfather, Hiroki Saito, on the abandoned lower levels of Sidonia, he knows little of society and doesn't talk much. Once Hiroki died, he snuck up into the residential district of the upper layers and got caught trying to steal rice. After that, the Captain made arrangements for him to become a Guardian pilot cadet. Unlike other crewmembers of Sidonia, he's unable to photosynthesize and must eat daily.

Izana's gender is neither male nor female, Izana's appearance androgynous. Izana's the first person Nagate befriends on the surface. Izana acts friendly towards Nagate, though Izana also shows some jealousy towards Hoshijiro and Yuhata.

The young girl who encountered Nagate when he tried to steal rice in the residential district.

His skills are extremely fine, and he prides himself as one of the top cadets. He's also to become the 8th generation heir to Kunato Developments, and is extremely proud. He discriminates against Nagate and Izana, considering them "sub-humans", and doesn't think too well of the fact that Nagate is the one piloting the hero's Guardian, Tsugumori.

11 clones rapidly grown in artificial amniotic fluid and given accelerated educations. All sisters share the exact same appearance. Their appearance and intelligence differ little from the other cadets, but they are only about 5 years old.

A suddenly transfers into the Guardian Pilot Training Academy, 628th generation. Her older brother is a member of Sidonia's most distinguished strongest Guardian unit, the Akai squad. Her hobby is building plastic models of Guardians.

Guardian Pilot Cadet, 628th generation. A studious young woman, who achieved her position as a cadet through hard work, so she holds some antagonism towards Nagate and Izana who got their assignments under special conditions.

A female pilot appointed as leader during their deployment. Her skill and popularity are unmatched, and she's very popular with the male pilots. More than a few of them want to photosynthesize with Samari, but she doesn't doesn't let it bother her.

Commands the Guardian squads under Captain Kobayashi.

The 28th Captain of Sidonia, and commander in chief of the Sidonian forces. She wears a mask resembling a deadpan face in front of civilian crew members. Calm and level-headed, she's capable of making the tough calls for the sake of Sidonia.

Captain's Assistant. Aide to Captain Kobayashi and the young man responsible for Nagate's care.

Dorm mother of the pilot dorms. She's a bear-type dorm mother in charge of running the dorm for pilots and cadets. She's usually very nice, but she gets mad when people call her by her first name, “Lalah”, and her wild instincts are let loose.