- Nell – The story's protagonist, from the viewpoint of the novel as a coming-of-age story. She is born to Tequila, a lower-class single mother, and, with the help of the nanotech Primer, grows up to become an independent woman and the leader of a new phyle.
- Harv – Nell's older brother, who plays an important role in the beginning as her protector; he obtains the Primer for his sister by mugging John Percival Hackworth. Harv is forced to leave Nell when she is accepted by the Neo-Victorians, and is later bedridden by asthma caused by the inhalation of dead nanomachines ("toner") in his childhood.
- Bud – A petty criminal and "thete", or tribeless individual, Bud is Tequila's boyfriend and Nell and Harv's father. He is obsessed with his muscular body, and possesses a cranial weapon implant (known as a "skull gun"), which he uses to mug people. When he robs a couple who are members of the powerful Ashanti phyle, he is executed for this crime early in the novel.
- Tequila – Nell and Harv's neglectful thete mother. After Bud's death, she has a series of boyfriends who mistreat the children to varying degrees.
- John Percival Hackworth – The novel's second protagonist. He is a Neo-Victorian nanotech engineer, and develops the code for the Primer. He makes an illicit copy of the Primer for his daughter Fiona, who is Nell's age. When his crime is detected, he is forced to become a double agent in a covert power struggle between the Neo-Victorians and the Chinese Celestial Kingdom. Hackworth is forced to spend ten years with a colony of "Drummers," using their distributed intelligence (similar but not identical to distributed artificial intelligence) for the development of a new form of nanotech, known as the Seed.
- Fiona Hackworth – Hackworth's daughter, and his motivation for stealing a second copy of the Primer. During Hackworth's decade-long exile with the Drummers, he is able to maintain a connection with his daughter through the Primer, and when he returns she joins him, eventually choosing to stay with a surrealistic acting troupe in London.
- Gwendolyn Hackworth – Hackworth's wife and Fiona's mother, who divorces Hackworth during his long absence.
- Lord Alexander Chung-Sik Finkle-McGraw – A Neo-Victorian "Equity Lord" with the Apthorp conglomerate, who commissions the development of the Primer for his granddaughter Elizabeth.
- Elizabeth Finkle-McGraw – Lord Finkle-McGraw's granddaughter. It was for her that the project to develop the Illustrated Primer was begun. However, she never became as engrossed in the stories created by the Primer as Nell, and later rebelled against her Neo-Victorian upbringing due in part to the abuse by Miss Stricken, one of her teachers. Elizabeth runs away from her wealthy aristocratic family to join the secretive CryptNet phyle. Lord Finkle-McGraw expresses satisfaction with this outcome to Carl Hollywood, deeming it akin to youthful rebellion.
- Judge Fang – A New York-born Chinese Confucian judge who sentences Bud to death in the beginning of the book. He also investigates Hackworth's mugging by Harv and his gang. As a civil official with deep Confucian principles, his decision to let Nell keep the stolen primer is one of the pivotal plot elements that allows Nell's story to unfold. The fallout from that choice leads him to question his allegiances to the Coastal Republic (which rules Shanghai and the surrounding area), and he eventually joins the inland Celestial Kingdom.
- Lieutenant Chang and Miss Pao – Judge Fang's assistants.
- Dr. X. – A mysterious character who evolves from being an illicit technology specialist and hacker to being a powerful Confucian leader and nefarious force. His name comes from the fact that most westerners cannot pronounce his Chinese name; he encourages people to instead call him by the first letter of his name.
- Constable Moore - Constable of the Dovetail community, semi-retired soldier, and Nell's adoptive father/guardian.
- Miranda Redpath – A "ractor" (actor in interactive movies) who, by performing in the stories of Nell's Primer, effectively becomes a mother figure for Nell.
- Carl Hollywood – A theatrical company director and Miranda's boss and adviser. He becomes more important towards the end of the novel, helping Miranda on her quest to find Nell, and aiding the escape of Coastal Republic refugees from the encroaching anti-Western Fists of the Celestial Kingdom. Nell appoints him as a trusted advisor of her new phyle.
- Miss Matheson – The head teacher at the academy where Nell, Fiona, and Elizabeth attend. She instructs Nell to find her own path.
- Miss Stricken – An authoritarian teacher at Miss Matheson's Academy who frequently uses corporal punishment on the students for minor infractions. During a confrontation with Nell, Stricken attempts to strike her with the ruler only to be immediately disarmed due to Nell's physical training by the Primer. This leads to her, Elizabeth and Fiona all being placed in detention, where they are forced to mindlessly copy from textbooks.
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