Jacob de Zoet
The main character of the novel. A young clerk who is sent to Dejima for his post in the Dutch East India Company to save money to marry his fiance, but whose life complicates with the encounter of Aibagawa Orito.
- Almighty Janitor: A clerk who becomes a main role in events concerning the future of The Napoleonic Wars and Japan as a country.
- No Celebrities Were Harmed: Based on Hendrik Doeff, the Dutch commander at Dejima from 1803-15, who among other things dealt with an English frigate attempting to force trade relations out of Japan, similar to Jacob.
- No Good Deed Goes Unpunished: Being honest does bring him a lot of trouble in his life.
- Unfazed Everyman: During the Phoebus arc, most definetly.
Dr. Lucas Marinus
The doctor working at Dejima, who despite his oddly anti-social behaviour is a humanist, and becomes a friend of Jacob.
- The Lancer: To Jacob, during the Phoebus arc.
- Omnidisciplinary Scientist: Not as extreme as some cases, but since he is leading the teaching of rangaku, Dutch Knowledge, to the Japanese at Dejima, he has to teach them about subjects far out of his expertise.
The commandant at Dejima who arrives along with Jacob in the beginning of the novel. Near the end of the first arc, he is revealed to be corrupt, and Jacobs refusal to comply with this leads to his demotion before Vorstenbosch leaves.
- Hypocrite: Near the beginning, he states that he and Jacob are probably the only honest men on Dejima. Come the end of the first arc, only Jacob is left.
- Karma Houdini: He never appears again after leaving Dejima at the end of the first arc.
- What Happened to the Mouse?: Disappears after leaving Dejima at the end of the first arc.
Melchior van Cleef
The second-in-command to Vorstenbosch, and later the commander of Dejima.
- Anti-Hero: Jacob doesn't particularly like him, but describes he is about as honest as they get in the company.
- Everyone Has Standards: Giving his dubious behavior to get promoted by Vorstenbosch earlier, one would expect he would immediately rat out Dejima to get a cushy deal with the British, but surprisingly, he refuses to deal with them.
- What Happened to the Mouse?: He never appears again after the Phoebus leaves Dejima. Given hsi refusal to cooperate with thim, it is likely prison awaited him on arrival in England.
A Prussian-born clerk at Dejima, who becomes second-in-command after Jacob is demoted by Vorstenbosch.
- Establishing Character Moment: He is introduced earlier, but the hint to his role later in the novel is given when he brutally beats van Cleef's slave for an undisclosed reason.
- Oh, Crap!: As soon as things don't go as he expects, this is his reaction.
- Politically Incorrect Villain: Granted, all the Europeans, including Jacob, keep slaves and are racist, but Fischer is the only to directly mistreat his, and his racism is definitely worse.
- Villainous Breakdown: When he realizes that neither the other Dutchmen nor the Japanese are willing to comply with his demands during the Phoebus incident, he suffers from this. Penhaligon notices it, and realizes just how pathetic Fischer really is.
A midwife, and a rangaku (Dutch Studies) student at Dejima. In the first scene of the novel, she saves the child of bugyo Shiroyama, and he rewards her by allowing her to study under Marinus at Dejima. Jacob falls in love with her, but before he can act, she is spirited away to the mountain cult of Abbot Enomoto, to be used as a midwife by him.
- Action Girl: Not explicitly, but her escape form Shiranui was pretty badass.
- Almighty Janitor: Similar to Jacob, a simple midwife becomes essential in big politics in Japan.
- Honor Before Reason: Her aborted escape attempt form Shiranui. She returned to make sure Yayoi could survive
- Wicked Stepmother: Her stepmother was the person who made it possible for Enomoto to kidnap her.
The abbot of Shiranui monastary, and the primary antagonist of the novel. He is responsible for kidnapping Orito, and his cult harvests human babies for a purported elixir of immortality.
- Bad Boss: Everyone around him is kept in an iron grip. The monks and nuns are kept addicted to drugs that will kill them as poison should they leave the monastary without his permission, and he is strongly implied to kill Shuzai and his mercenaries after dealing with Ogawa.
- Eats Babies: He is just that evil.
- Evil Gloating: Full of it, both to Jacob (indirectly), Orito, Ogawa before his death, and in the end, more like Unsportsmanlike Gloating to Shiroyama.
- Evil Old Folks: Very old, if he is to be believed.
- Hannibal Lecture: Delivers an excruciating one to Ogawa before killing him.
- Maybe Magic, Maybe Mundane: It is never stated outright if his magic tonics actually work.
- Out-Gambitted: Epically out-gambits Ogawa, but is then out-gambitted by Jacob and Shiroyama.
- Oh, Crap!: When he realizes his demise is near.
- People Farms: The truth about Shiranui.
- Really 700 Years Old: He claims to be 600 years old.
- Villainous Breakdown: After realizing he has been poisoned, he, with increasing despair and fear of death, babbles on about how what he is doing is right, nobody understands him, that he will live forever, and Ogawa and Shiroyama are worthless people. Then, he tries to draw his ceremonial dagger to attack Shiroyama before the poison takes effect.
One of the best interpreters at Dejima from a samurai family, who had previously been in love with Orito, but prevented form marrying her. He takes a major role in the second arc of the book, trying to rescue Orito from Shiranui.
- Hero of Another Story: at first, to Jacob. After his death, Jacob realizes it was not that simple.
- I Want My Beloved to Be Happy: He wanted Jacob and Orito to marry.
The magistrate (bugyo) of Nagasaki. His child is saved by Orito at the start of the story. Because of this, he feels he owes her a debt, and as Jacob later helps him save Nagasaki from the Phoebus, in order to pay them both back, he sacrifices his life to kill Enomoto and free the nuns and monks of Shiranui.
- Cool Old Guy: Fifty years old, but it still counts.
- Dying Moment of Awesome: Sacrifices himself to kill Enomoto. When he is certain that he had been poisoned, he calmly explained to him why he was getting killed.
- Go-Karting with Bowser: Regularly plays go with Enomoto. Granted, that was before he realized he was a complete psychopath.
- No Celebrities Were Harmed: He is based on the magistrate of Nagasaki during the Phaeton Incident of 1808, Matsudaira Yasuhide, seeing as the Phoebus arc takes a lot of inspiration from this incident, including the understaffing of samurai ready to defend Nagasaki, and Matsudaira's suicide after the incident, the difference being that the historical Matsudaira committed suicide to repent for not having the sufficient defenses ready at Nagasaki, while Shiroyama in the book does it to take down Enomoto without tainting his family's name, and thereby ruining the life of his young son.
- Took a Level in Badass: For most of the novel , he is merely a background character. Not so much when Jacob reveals to him what Enomoto was doing. Rather than being on Enomoto's payroll like Shuzai was, and murdering Jacob, he sacrifices his life to kill Enomoto and free the captives at Shiranui.
The old fencing teacher of Ogawa, whom he enlists in his attempt to rescure Orito. Turns out to be an accomplice of Enomoto, and betrays Ogawa.
- False Friend: Betrays Ogawa to Enomoto.
- Rewarded as a Traitor Deserves: Implied to have been killed off by Enomoto after the death of Ogawa. The report Jacob receives states that 11 bandits (fitting with Shuzai and his ten men) had been tortured to death as penalty for Ogawa's death by Enomoto, and he is never seen again after that.
A nun at Shiranui, whom Orito developes a friendship with, and is the only thing that makes her life bearable at the monastary. She has fox-like pointed ears, similar to a kitsune.
- Heterosexual Life-Partners: Developes a friendship with Orito, and as they visit Dejima together ten years after gaining their freedom, they are strongly implied to have a close relationship for life.
The captain of the Phoebus, and the leader of the ship's attempt to open relations with Japan.
- Anti-Villain: While he is an antagonist to Jacob, his backstory is kind fo sympathetic. His wife and only son are dead, and his career is waning, the reason why he is desperately trying to revive it with the Japanese mission.
- Mighty Whitey: Obviously perceives himself as this.
- No Celebrities Were Harmed: Similar to Jacob being inspired by Hendrik Doeff and S Hiroyama by Matsudaira Yasuhide, Penhaligon is this to Fleetwood Pellew, the captain of the Phaeton during the incident in 1808 which served as an inspiration for the events of the third arc, although his resemblence to Pellew is somewhat less obvious, as Pellew was only 19 at the time of the incident, while Penhaligon is closing in on retirement.
- One Last Job: His Nagasaki mission is meant to be this before his retirement.
- Red Right Hand: His podagra in the left foot, with makes him more and more crippled as the novel progresses.
- Sore Loser: When he realizes he cannot open relations to Japan as hoped, he decides to bomb the crap out of Dejima.
- You Remind Me of X: The reason he cannot bring himself to kill Jacob is because he reminded him of his late son.
- What Happened to the Mouse?: After failing to give the order that would kill Jacob, he leaves Nagasaki, and his fate is not revealed. During the epilogue, Jacob himself wonders what has happened and wishes he could have met him, but concludes that he probably died long ago.
The former commander of Dejima, who is relieved of his command at the start of the novel by Vorstenbosch due to corruption, but returns as the instigator of the Phoebus incident later on, as part of Penhaligon's crew.