Lucky Jack Aubrey, Goldilocks, a tall, blond beefy Englishman, at sea since he was eight years old, beloved by his men, rather less so by his superiors. A lion at sea, and particularly inept on land.
Acrofatic: He's described as somewhat heavy, but he's extremely nimble and coordinated as a result of a life at sea.
A Father to His Men: He feels it strongly when any of his men die, and takes a personal and abiding interest in the lives and careers of his personal followers and officers. This is particularly true of his midshipmen (the "squeakers"), who come to him at a very young age and whose education and moral upbringing he takes a direct hand in.
A Man Is Always Eager: This gets him into a great deal of trouble personally and professionally beginning with the first book and lasting much of the series. It's less that he's a slut and more that he's spent his entire life at sea and has no clue how to behave on land (let alone say "no".)
Animals Hate Him: Although people tend to love him, he simply cannot catch a break with animals. Horses throw him, a wombat eats his hat, and he has to get a sloth drunk to keep it from wailing in despair at the sight of him.
The Chains of Commanding: Jack has to write letters home to the parents of the officers and the midshipmen killed under his command. Additionally, the authority of the position means that it's nearly impossible for a captain and his officers to really become friends, a kind of social burden that falls on Jack quite often.
Clueless Chick Magnet: At a party, two women are talking about the beautiful man. Jack turns around to see who they're talking about. He honestly has no idea.
Companion Cube: The violin he's had since he was a boy. He's distraught when it breaks.
Cultured Warrior: Jack is incredibly fond of music, and as an adult has taken to math and astronomy like a fish to water.
The Drunken Sailor: Occasionally the result of a really good party, it only gets him into trouble once or twice, usually ashore.
Eek, a Mouse!!: Well, a Snake. Jack Aubrey has a serious fear of snakes, and at one point in Master and Commander jumps up onto a chair when one crawls into the room, not coming down until Stephen removes it. Stephen doesn't help matters any by being a Deadpan Snarker about it, pulling Jack's leg about the (nonpoisonous) snake being a deadly and aggressive viper.
Genius Bruiser: Jack is a tall, burly, heavily scarred war hero and immensely successful naval commander. He is also, along with his good friend Dr. Maturin, a Fellow of the Royal Society (Britain's most prestigious academic society). He has written a number of well-received papers on astronomy and geometry, and built his own observatory and telescopes.
Genius Ditz: For all his incredible talent as a navigator, seaman, and man of war, Jack is spectacularly incompetent ashore, getting himself into every kind of trouble imaginable.
Get Rich Quick Scheme: Some of Jack's problems involve falling for one of these. Fortunately, he managed to give his wife power of attorney, putting everything in a tangle and keeping him from complete destitution.
Historical-Domain Character: Master and Commander in particular was heavily based on the real-life exploits of Captain Cochrane (particularly the Sophie-vs-Cacafuego/Speedy-vs-Gama duel, accurate down to the number of guns and the number of crew), who really was captured by Christy-Palliere in the same way that Jack Aubrey was captured—and the real-life Christy-Palliere was so impressed by Cochrane's exploits that he refused to accept his sword in surrender, the same as with Aubrey.
If I Were a Rich Man: Jack wasn't born into poverty, but he also never had money, and spends much of the series wishing he were rich, and usually doing exactly the wrong thing to get that way.
In-Series Nickname: Aubrey is referred to as "Goldilocks" by the crew (though never to his face, of course), for his blonde hair. In the wider world, he's well known as "Lucky Jack Aubrey" for his good fortune in capturing prizes.
Living Legend: Captain Jack Aubrey, globe-trotting badass much caressed by the Admiralty, astronomer and geometer, member of the Royal Society.
Mixed Metaphor: Jack couldn't keep an aphorism straight if it walked in the room and put a bird in the bush.
Mugging the Monster: Someone demands of an unhappy Jack, "Your money or your life". It doesn't end well for the erstwhile cutpurse.
Must Have Caffeine: While he's not as bad as Stephen, Jack is inhuman without his morning coffee.
Nautical Folklore: For all he insists he's not, and for all he's a very scientific sailor, Jack is still ridiculously superstitious, at one point spending weeks taking the ups and downs in the recovery of a particularly ill sailor as an omen for the success of an entire naval campaign.
Perpetual Poverty: Jack's money will never last. He's a genius at sea and completely at a loss ashore.
Privateer: During a particularly low point in his career, Jack ends up one of these.
Reasonable Authority Figure: He's "no friend to the cat", meaning the cat of nine tails, meaning he prefers not to have his mean beaten for punishment unless discipline starts to go by the wayside. He likes a taut ship, but a taut ship and a happy ship go hand in hand.
Remember When You Blew Up a Sun?: Despite a star-studded career, people mostly remember Jack's first absurd success, taking the Cacafuego with a ship half her size.
Renaissance Man: astronomer/telescope builder/mathematician/Member of Parliament/musician
Stout Strength: He weighs about 18 stone (~250 pounds), and Dr. Maturin often frets about his weight and tries to get him to eat less. But he's still fit enough to lead his crew into hand-to-hand battles and scramble up the ship's ropes like an ape. If you have ever tried to climb up a sailing ship's rigging, you will grasp that he is, even by modern standards, quite physically fit. Jack is quite tall (his exact height isn't recorded, but is probably at least 6 feet, in a period where most men were under that; Napoleon is always depicted as being short but was probably actually of average or slightly less-than-average height for the time). His 18 stone probably doesn't hang on him in such an unseemly manner as might be supposed by modern readers.
Ugly Guy, Hot Wife: Though a good-looking man in general, Aubrey is covered in scars, including missing most of his right ear (getting it reattached is almost a Running Gag), and when you consider his wife...
Wooden Ships and Iron Men: Almost literally; he practically rattles when he walks, he's got so many bits of metal floating in his various scars.
Worthy Opponent: Jack accumulates these, whereas Stephen tends to cut their throats.
Dr. Stephen Maturin (Sr. Esteban Maturin y Domanova)
In the first book, Stephen is something of a genius ditz and Audience Surrogate. He gets more fleshed out starting in the second book, as a physician, as a lover, as a fighter, and as a badass secret agent. From then on, he's reliably the Deuteragonist, if not a second protagonist.
Addiction Displacement: As soon as he swears off the alcoholic tincture of laudanum, he purchases some coca leaves. Purely for medicinal purposes.
Ambiguously Bi: He tells Diana in Post Captain that he is "not in the least degree interested in women as such. Only in persons." He is thought to be gay several times, his tolerance is stated loudly just as often, and there are further ambiguities in the text.
Audience Surrogate: His main purpose in the first book was to have all things nautical explained to him so the audience wouldn't be completely at sea. We still tend to drown in jargon. This declines later and he comes into his own and other surrogates come and go.
Autopsy Snack Time: Whereas Jack is a stickler for cleanliness, Stephen will frequently eat while surrounded by the decaying remains of his collection (including gallows-corpses he bought for sixpence).
Badass Bookworm: He's 5'6", gaunt, clumsy, "small, indefinably odd and even ill-looking" man as well as a doctor, polyglot, natural philosopher and all-round intellectual. He is also Britain's greatest spy. Over the course of the books he is seen shooting the pips out of playing cards, winning several duels, operating on himself, and dispatching his enemies in very badass ways. And then dissecting them.
Berserk Button: It's always dangerous to disparage the Irish and the Catholics around Stephen, who is both. He doesn't mind when Jack occasionally puts his foot in his mouth with anti-Catholic sentiment, though, since he knows Jack never does it intentionally, and he always apologizes for it.
Celibate Hero: At one point, so celibate that the Admiralty was worried he might be a blackmail target by foreign intelligence services. Then he had a love affair go badly (with a woman), and so they were relieved.
Cloudcuckoolander: He may be able to speak half a dozen languages and cut your head opennote on purpose without killing younote also on purpose, but god help him if he tries to do anything else. The sailors view him as just this side of completely helpless.
Cool Shades: He frequently wears glasses with colored lenses. This helps him win at cards. It also helps him be the best intelligence agent in the Empire. It also helps disguise his distinguishing feature, his pale, almost reptilian eyes.
Cultured Warrior: Stephen plays the cello and attends the opera. At sea he prefers to be a physician and natural philosopher, professionally, though this also acts as a cover for his intelligence work, which occasionally sees him fighting for his life and enduring Cold-Blooded Torture.
Dark and Troubled Past: Stephen is illegitimate and an orphan, fostered in the back of beyond, sent from uncaring relative to relative, spends time in several prisons in Spain and Portugal, a Catholic who goes to a Protestant university in his mid-teens, survives the Terror, flees to Ireland, survives the 1798 rebellion, loses Mona, loses Lord Edward Fitzgerald, becomes a fugitive, and ends up penniless. All before the first page of the first book. As an adolescent, he also spends "a long time" locked in a prison cell with a convicted rapist.
Deadly Doctor: He'll go to the ends of the earth to keep you alive if you're his patient. But test his patience and he can kill you with sword, pistol, or notebook.
Deadpan Snarker: To Jack's lame punnery. In the second book, he shows a flash of wit that continues to amaze and delight the Navy until the end of the series, twenty books later. Not the wit mind you, the very same joke continues to delight.
Deconfirmed Bachelor: A good example of the trope. As a philosopher, he has no particular attachment to the married state, and many view him as likely to be a lifelong bachelor, what with being a very odd, very solitary man. His eventual marriage really does surprise the hell out of everyone. That he and his wife maintain separate residences cause them to nod wisely.
Destructive Romance: His affair with laudanum begins at roughly the same time as his affair with Diana.
Impoverished Patrician: He owns a castle and earns a few hundred pounds a year just from rent, but the castle is in disrepair and, anyway, it's in Spain. When we first meet him, he's completely broke, wondering how he's going to get back to England from Gibraltar, and also wondering whether to eat or sleep well that night.
Informed Self Diagnosis: Stephen is generally quite good at this, with the notable exception of failing to diagnose his own addiction to laudanum.
The Klutz: Stephen somehow contrives to get into accident after accident at sea, ranging from falling out of the boat to somehow turning a complete somersault in a particularly violent sea. As a result, the seamen around him look upon with real affection and considerable respect for his medical prowess—and stand wary in case he manages to take yet another improbable tumble.
La Résistance: A passionate member in his youth, fighting for Irish independence.
Money To Throw Away: A few times, he manages to acquire a good sum of money, and is usually happy to throw it at the nearest friend. The earliest may be when a wealthy and foolish Marine insults a woman Stephen likes and so Stephen takes him for a year's pay at cards.
Stephen can always be counted on to lend Jack a few pounds, and has been known on occasion to simply point Jack at wherever he's storing his bankroll and tell him to peel off whatever amount he needs. This leads to a funny moment on at least one occasion, when Jack goes to get Stephen's bankroll out of his coat and is appalled both at its size and that Stephen is carrying it around without any sort of protection or concealment.
He uses this to get out of a potentially sticky situation early on in the series, when he and Jack are visiting Christy-Palliere during the brief Peace of Amiens; Stephen is caught snooping around a French naval base, but talks himself out of trouble (with a bit of help from Jack) by explaining that he was tracking down a rare local bird.
Perpetual Poverty: Less so than Jack, as he has a Spanish castle to fall back on, and he doesn't really care about money, but he fell in with Jack at a good time and his fortune tends to rise with Jack's.
Running Gag: Stephen's complete inability to board a naval vessel.
Smart People Know Latin: Maturin will often use Latin around patients both to keep them from knowing what he is saying (when he is talking to another physician or an assistant who also speaks Latin) and because patients are reassured by the fact that their doctor is learned enough to speak Latin. The crews of the ships he serves on often brag that their ship has a real physician who speaks Latin and Greek.
Sugar and Ice Personality: Partly by personal inclination, but also professional (he's required to be secretive both as a physician and a spy), he's cold and distant with most people. Those few who get close to him discover he's incredibly warm and caring. Even they don't really know the full depth, as they see him as an incredibly competent, contained, and certain figure, little knowing the vasty sea of passion and doubts within.
Ugly Guy, Hot Wife: Stephen is generally described by himself and the narrator as a dark, scrawny, ill-looking man, but women generally find him attractive, suggesting he's more of a Byronic Hero.
Broken Bird: Her determination to win a husband and willingness to use sex to get him ends up destroying her reputation and leading her into the power of unscrupulous men, until she's desperate to get away. And all that's after her father and husband die in India.
Cool Big Sis: Of a sort, to Sophia. She's a few years older and a war widow who grew up in India, whereas Sophia is a sheltered naïf who cried to learn men had hairy chests. Diana's the cynical slut variety.
Cry into Chest: During a moment of despondency in India, she gets comfort from Maturin. Then Canning walks in and violence ensues.
Distracted by the Luxury: Given to be the reason she keeps throwing over Stephen for other men. She doesn't just want any old marriage, she wants to marry a wealthy man. "Love in a cottage" isn't her style.
Does Not Like Men: She views men as the enemy, figuring they're just out to screw her (literally) so she has to do what she has to do to get by. Stephen is her only male friend.
First Girl Wins: She's not the first girl Maturin meets, but she is the first he shows any interest in.
Gamer Chick: Nineteenth century version; we meet her riding a horse on a fox hunt.
Girl in the Tower: While living with her crazy cousin, she has a room on the second floor. At one point Jack, visiting late at night, climbs up to visit her.
Kissing Cousins: A crazy cousin she was sent to take care of to get her away from the men courting the Williams daughters
The Lad-ette: To a degree. She drinks, swears, rides, games, fucks.
Sleeps with Everyone but You: To Stephen, because she actually values his friendship and doesn't see him as a potential husband, ironically. Maybe. The text states that they kissed a few times, so it's hard to know what they might have done.
Smells Sexy: Stephen gives her a bottle of scent in the first book, a gift he greatly regrets as it keeps showing up on other men.
Slut Shaming: A penniless widow, she rather transparently uses her charms to befriend men in the hopes of securing a second marriage. This does absolutely nothing for her reputation in England, and she bounces from her cousin's home, to her mad cousin's home, to the care of a Jewish merchant in England (where she's friends with the notorious mistress of the Prince of Wales), to the care of the merchant, only in India, to the care of an American businessman in Boston, to a respectable marriage to an Irish-Spanish bastard orphan physician. Still, at least she's finally an honest woman.
Wartime Wedding: As part of her confused relationship with Johnstone, she gave up her British citizenship, which leads to problems when she wants to return during the war of 1812. She and Stephen quickly get married to rectify that.
Sophia's mother, Diana's aunt, Jack's mother-in-law. She's conniving, bitter, a pain in the ass, and she will see her daughters well set up in good marriages or she'll die trying.
Evil Matriarch: No one who knows her is at all fond of her. With the exception of her grandchildren, the only people she shows any kindness to.
Pet the Dog: Despite her overall nastiness, is quite fond of her grandchildren.
Stephen and Diana's only child.
Ambiguous Disorder: she's very quiet and self-contained as a young child, and some readers speculate that she might be autistic by modern standards.
Benevolent Boss: a close friend of Stephen's, as well as his boss. Both are naturalists and entomologists of rare dedication and skill, which provides a cover for their meetings. Plus, Blaine's influence is essential in getting Jack reinstated.
Lovable Sex Maniac/Dirty Old Man: one comical subplot is his rediscovery of his sex drive and his asking advice from Stephen on whether or not to marry the young lady that he's courting.
10-Minute Retirement: Blaine's enemies—including Wray and Ledward—force him out of his job as intelligence chief by the time of The Reverse of the Medal. Fortunately, as Blaine himself notes, he still retains many of his contacts at the highest level of government, and with their help he slowly carries out his own hunt for the mole before Duhamel's defection to Stephen closes the net. After that, he pulls a Smiley and returns to his post as head of intelligence.
The Captain: A long-time friend of Aubrey since their days as junior officers.
The admiral under whom Aubrey first served as a commander.
A gentleman whose gambling losses lead him eventually to cheating and to trading British secrets for French gold.
Bury Your Gays: He and his lover/accomplice Ledward end up being shot and then dissected by Maturin and his anatomist friend Van Buren.
The Mole: Does considerable damage to England's secret service efforts until he is discovered.
Villainous Breakdown: a long, drawn-out one, but there nonetheless. Though we first meet him in Desolation Island, we get to know him in detail in Treason's Harbour, where Wray appears to be a competent and dangerous double agent, albeit one with a gambling addiction and a growing drinking problem. By the time he re-appears in The Reverse of the Medal, Wray is a confirmed drunkard who is nearly insolvent due to gambling debts. By the time that Stephen meets him for the last time in The Thirteen-Gun Salute, Wray is completely useless, with the French deciding that Ledward is a better agent (he is) and Wray being allowed just enough of an income to live.