Yes, I’ve started reading *that* novel and I’m quite helpless when it comes to boat lingo.
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In modern day, there is no difference. Captain is the most common. In the oooooold days (hundreds of years ago, say, 17th-18th century), “Master and Commander” was a specific rank. Usually people who were captains of specific types of ships were actually granted this rank. In the late 18th century, it got simplified to just “Commander”.
In the modern Navy (US and I believe Royal as well), “Commander” is rank O-5, one lower than “Captain” (O-6). These are ranks, but a Commander can still be a “captain” by virtue of having command of a ship.
Initially ranks were not ranks, they were positions. Lieutenant was also not a rank, but the position of the assistant to the captain. A major ship might have multiple lieutenants, with the most senior being the first lieutenant, the next the second lieutenant, next the third lieutenant.
A captain commanded a major ship, frequently with the help of a sailing master.
A small combatant didn’t require a captain, nor the addition of a separate master. The master and commander was the position for those ships.
Eventually positions became ranks, but the historical role is still present in the name. Master and commander was simplified to just commander.
More fun facts: lieutenant derives from the French for placeholder for a superior.
In the film, the sailing master is portrayed by the character John Allen (“Mr Allen”). In the books, it gets a bit more complicated as Aubrey sometimes does and does not always hold both ranks.
Mr Allen is a sailing master which means he’s primarily responsible for navigation. He’s actually picked by Aubrey himself because of his sailing experience as a whaler in the Pacific.
Historically, sailing masters were warrant officers (not commissioned officers, but still an officer) and were held in high regard. They were the most knowledgeable on mathematics and navigation and were also entrusted to train and mentor midshipmen.
Aubrey was the Surprise’s commander (highest rank aboard the ship) and Allen was its sailing master. While there were two lieutenants underneath Aubrey, Allen would have also held a small command and could do things such as lead a watch, issue orders to his own seamen, lead parties, and even take command of prize ships if needed.
So if Aubrey was a tactician, Allen was a hybrid navigator/engineer. In the Age of Sail, Allen would be charged with understanding the sails and rigging because that’s how you point the ship and move it in the right direction.
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