The captain was the supreme head of the ship, empowered to displace any inferior officer except the master (Monson). He was not always competent to navigate (ibid.), but as a rule he had sufficient science to check the master's calculations. He was expected to choose his own lieutenant (ibid.), to keep a muster-book, and a careful account of the petty officer's stores (Monson and Sir Richard Hawkins), and to punish any offences committed by his subordinates.

A lieutenant seems to have been unknown in ships of war until the early seventeenth century. He ranked above the master, and acted as the captain's proxy, or ambassador, "upon any occasion of Service" (Monson). In battle he commanded on the forecastle, and in the forward half of the ship. He was restrained from meddling with the master's duties, lest "Mischiefs and factions" should ensue. Boteler adds that a lieutenant ought not to be "too fierce in his Way at first ... but to carry himself with Moderation and Respect to the Master Gunner, Boatswain, and the other Officers."

The master was the ship's navigator, responsible for the performance of "the ordinary Labours in the ship." He took the height of the sun or stars "with his Astrolabe, Backstaff or Jacob's-staff" (Boteler). He saw that the watches were kept at work, and had authority to punish misdemeanants (Monson). Before he could hope for employment he had to go before the authorities at Trinity House, to show his "sufficiency" in the sea arts (Monson).

The pilot, or coaster, was junior to the master; but when he was bringing the vessel into port, or over sands, or out of danger, the master had no authority to interfere with him (Monson). He was sometimes a permanent official, acting as junior navigator when the ship was out of soundings (Hawkins), but more generally he was employed temporarily, as at present, to bring a ship into or out of port (Monson and Boteler).

The ship's company was drilled by a sort of junior lieutenant (Boteler), known as the corporal, who was something between a master-at-arms and a captain of marines. He had charge of the small arms, and had to see to it that the bandoliers for the musketmen were always filled with dry cartridges, and that the muskets and "matches" were kept neat and ready for use in the armoury (Monson). He drilled the men in the use of their small arms, and also acted as muster master at the setting and relieving of the watch.

The gunner, whose duties we have described at length, was privileged to alter the ship's course in action, and may even have taken command during a chase, or running fight. He was assisted by his mates, who commanded the various batteries while in action, and aimed and fired according to his directions.

The boatswain, the chief seaman of the crew, was generally an old sailor who had been much at sea, and knew the whole art of seamanship. He had charge of all the sea-stores, and "all the Ropes belonging to the Rigging [more especially the fore-rigging], all her Cables, and Anchors; all her Sayls, all her Flags, Colours, and Pendants;[23] and so to stand answerable for them" (Boteler). He was captain of the long boat, which was stowed on the booms or spare spars between the fore and main masts. He had to keep her guns clean, her oars, mast, sails, stores, and water ready for use, and was at all times to command and steer her when she left the ship (Hawkins). He carried a silver whistle, or call, about his neck, which he piped in various measures before repeating the master's orders (Monson). The whistle had a ball at one end, and was made curved, like a letter S laid sideways. The boatswain, when he had summoned all hands to their duty, was expected to see that they worked well. He kept them quiet, and "at peace one with another," probably by knocking together the heads of those disposed to quarrel. Lastly, he was the ship's executioner, his mates acting as assistants, and at his hands, under the supervision of the marshal, the crew received their "red-checked shirts," and such bilboed solitude as the captain might direct.

The coxswain was the commander of the captain's row barge which he had to keep clean, freshly painted and gilded, and fitted with the red and white flag—"and when either the Captain or any Person of Fashion is to use the Boat, or be carryed too and again from the Ship, he is to have the Boat trimmed with her Cushions and Carpet and himself is to be ready to steer her out of her Stern [in the narrow space behind the back board of the stern-sheets] and with his Whistle to chear up and direct his Gang of Rowers, and to keep them together when they are to wait: and this is the lowest Officer in a Ship, that is allowed to carry a Whistle" (Boteler). The coxswain had to stay in his barge when she towed astern at sea, and his office, therefore, was often very wretched, from the cold and wet. He had to see that his boat's crew were at all times clean in their persons, and dressed alike, in as fine a livery as could be managed (Monson). He was to choose them from the best men in the ship, from the "able and handsome men" (Monson). He had to instruct them to row together, and to accustom the port oarsmen to pull starboard from time to time. He also kept his command well caulked, and saw the chocks and skids secure when his boat was hoisted to the deck.

The quartermasters and their mates had charge of the hold (Monson), and kept a sort of check upon the steward in his "delivery of the Victuals to the Cook, and in his pumping and drawing of the Beer" (Boteler). In far later times they seem to have been a rating of elderly and sober seamen who took the helm, two and two together, in addition to their other duties. In the Elizabethan ship they superintended the stowage of the ballast, and were in charge below, over the ballast shifters, when the ships were laid on their sides to be scraped and tallowed. They also had to keep a variety of fish hooks ready, in order to catch any fish, such as sharks or bonitos.

The purser was expected to be "an able Clerk" (Monson) for he had to keep an account of all provisions received from the victualler. He kept the ship's muster-book, with some account of every man borne upon it. He made out passes, or pay-tickets for discharged men (ibid.), and, according to Boteler, he was able "to purse up roundly for himself" by dishonest dealing. The purser (Boteler says the cook) received 6d. a month from every seaman, for "Wooden Dishes, Cans, Candles, Lanthorns, and Candlesticks for the Hold" (Monson). It was also his office to superintend the steward, in the serving out of the provisions and other necessaries to the crew.