Jacob de Zoet
The protagonist of the story, Jacob de Zoet is a devout, honest young Dutch clerk with high hopes, a full head of red hair, and more integrity than the rest of the Dutch East Indies Company put together. He is loyal, steadfast, curious, reasonable, and even brave when the time comes. Admittedly, he is often swayed by quick infatuations, and his promises are often made a bit hastily, but his intentions are almost always pure.
Orito Aibagawa
Orito, Jacob's primary love interest in the bulk of the novel, is an intelligent young Japanese woman who studies at the medical academy of Dr. Marinus while not performing her duties as a capable midwife. She is distinguished by a burn mark on her cheek, which is said to limit her suitability for marriage, but which Jacob finds intriguingly appealing. Orito is, if not braver, than at least more decisive than Jacob, and her ingenuity in her escape is countered by her loyalty to her friends.
Lord Abbot Enomoto
Enomoto begins the novel as a suspicious figure and slowly blossoms into what appears to be the manifestation of evil incarnate. He is a crafty, manipulative, and abhorrently selfish man who leads a dark cult, which deals in the murder and consumption of newborns, stealing their lives to feed his own power. Through shrewd schemes, he also has economic leverage on Nagasaki, and through no one knows of his true nature, they would still be unable to challenge him for fear of their own lives.
Ogawa Uzaemon
Uzaemon, one of Jacob's few friends in Dejima, is a Japanese interpreter with a good heart and an interesting in learning. He is a samurai, as his family is one of nobility in Nagasaki, and he also loves Orito Aibagawa, risking (and giving) his life in an attempt to free her from her captivity.
Dr. Marinus
One of the novel's most inscrutable characters, Dr. Marinus is a cranky old European doctor who instructs students on Dejima in medicine. His interests, however, lie far beyond medicine, as does his area of respect. Although grumpy on first encounters, Dr. Marinus eventually reveals himself to be as brave as anyone, standing firm with de Zoet on the tower as the English fire cannonballs at them.
What a casual reader of The Thousand Autumns of Jacob de Zoet might not know about Marinus is that he is far more important than he might seem; he appears centuries later in David Mitchell's novel The Bone Clocks, where it is revealed that his nature is more mysterious and complicated than that of an ordinary mortal.
Unico Vorstenbach
Chief Vorstenbach is the new head of the Dejima branch of the East Indies Company at the novel's inception, and Jacob harbors great respect for him. It eventually comes to light, however, that Vorstenbach is no better than the old Chief, perhaps even worse, and he has no intention of reforming the corruption that has become so rampant in their company.
Captain John Penhaligon
Captain Penhaligon is the commander of the English ship that comes to wrest the Japanese trade route from its current Dutch holders. His gout-ridden leg gives him serious pain, but he still maintains a firm exterior for his men. Penhaligon isn't afraid of using violence to achieve his ends, but when he sees de Zoet standing strong in the face of the English cannons, he is reminded of his own son and calls off the attack, retreating back to England.
