Up until the Elizabethan Era, vessels were not built exclusively for war, and performed dual service in peacetime as merchant vessels. The senior mariner in charge of general operation of a vessel was the ships Master Mariner, also referred to as Sailing Master, or simply Master. The ships master might or might not actually own the ship, but was in command while underway. This was not an expression of ownership of the sailors aboard, but of his mastery of the art and science of ship handling and navigation. The ships master might or might not actually own the ship, but was in command while underway.

During wartime, vessels were used to transport troops from port to port, who embarked from there to march forth into battle. Later, ships were modified for war by addition of a Fore Castle and a After Castle, raised wooden stockades with the appearance of a castle wall, complete with crenellations, or alternating raised sections, to offer concealment to archers. This allowed the soldiers to fight from the ship while underway. The embarked soldiers were commanded by a Captain, who was placed in overall command of the vessel.

During the 1600s, the hierarchy of command was codified for naval vessels. As said before, the Captain was in charge of the vessel. Below him in the chain-of-command were several Lieutenants, ranked in order of succession in case of the Captains death. The First Lieutenant was second in command, and so on for the rest. In the English navy the First Lieutenant was, and even today often is, referred to as Number One. The number of Lieutenants was based on the size of the ship and crew.

Aboard most larger warships, the crew was divided (billeted) into six Divisions:

- Focslemen (Forcastlemen); who handled all equipment to raise/lower anchors, set headsails forward of the foremast, man the forward guns, and sound the depths ahead of the ship. These were the most experienced sailors, and were under the charge of the First Lieutenant.

- Waisters; These were the very inexperienced or very old sailors stationed on the middle of the deck, handling sails and amidships guns; these were under the charge of the Second Lieutenant, and could be overseen by the Captain himself from the Quarterdeck.

- Afterguard; Marines were stationed on the Quarterdeck to protect the Captain during battle. Marines were also trained to operate the quarterdeck guns, and help sailors work the sails. - Foretopmen, Maintopmen, or Mizzentopmen; These three Divisions handled sails from aloft in the rigging. These men were supervised by the Captain of the Foretop, Captain of the Maintop and Captain of the Mizzentop, who were senior Petty Officers.

Each Division was further divided into Larboard and Starboard Watches, who would alternate between working and resting under normal sailing. Everyman in the crew has specific jobs to do under specific circumstances (Mooring, Battle Stations, Fire, Rescue, boat lowering, etc.), all outlined in detail on the Watch, Quarter and Station Bill (WQSB). Failure to know and man ones proper stations was a punishable offence.

During this period, most naval vessels were not kept on active service during peacetime in order to reduce the cost of operating, victualling, and pay. Most ships were anchored in an estuary or river, called In Ordinary status. A small maintenance crew tended to the assembled ships, effecting minor repairs to hull, sails, and rigging, to ensure their readiness if and when another war required them.

The discharged crewmen were sent ashore; Officers were given half-pay as encouragement to remain ready to return to their duties when needed. Captains tended to rely of their pay to sustain themselves in their homes. Junior lieutenants tended to join the merchant fleet to supplement their half pay; those officers might not be available to re-man vessels being returned to service. The sailors were discharged completely to fend for themselves, as most could either volunteer or be pressed into service in wartime.

When a war began, for the reasons above, there would be a shortage of junior officers to occupy all of the leadership positions aboard. (Lieutenants were usually given a personal letter of Commission from the Admiralty to serve as a Commissioned Officer in the Navy). To resolve this shortage, the English (later, British) Admiralty would post a bulletin, or warrant, on a notice board outside the headquarters building. This Warrant offered a position of Officer to very senior Petty Officers in their rated specialty (Sailing Master, Boatswain, Gunner, Carpenter, Surgeon, Purser); these officers were appointed by Warrant, rather than from Commission; hence the term Warrant Officer. Although Warrant Officers were often looked down upon by Lieutenants; certain Warrants were allowed to dine (mess) in the Wardroom, others had to mess with the crew.
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