The title of Captain is the title given to an individual in control of a ship at sea, either pirate, marine, or civilian.
The rank of a marine officer who commands a ship would not necessarily be "Captain" (大佐,Taisa?)", it may be higher (up to Fleet Admiral), or, on small ships, lower. Any officer below the rank of Taisa who commands a ship, is addressed as "captain" while aboard that ship, by naval custom. The ship's captain also may be referred to as the Skipper.
Pirate Captains are the ones who are at the very head of a pirate crew. Pirating captains also tend to be the mightiest members of their crew, and most of them tend to exploit their strength even over their own subordinates to ensure loyalty; though not necessarily, as anyone can attain the rank of captaincy out of pure leadership, as a founding member or voted by other crew members. All major decisions are made by them, though they may be usually advised and influenced by other members.
If multiple pirate crews were to form an alliance, the captains of the allied crews share equal standings, becoming co-leaders of the alliance. They thus have limited control over their allied crew's men, and when it comes to important decisions, their opinion must be included.
In a fleet, the captain that is in charge of it is referred to as 'admiral' (Teitoku, 提督) (or commodore in English dubs), while the captains of the subservient crews are known as 'division commanders'. When called upon by their admiral, the division commanders must follow their orders. However, when not under direct orders of the admiral, the captain is free to act as they please, provided their actions don't harm or cause trouble for the fleet.
In real life, captains of pirate crews were often elected to their posts by a ship's crew. Even if they owned the ship, if the captain fell out of favor with their crew, another could be elected without notice. Sometimes, inadequate captains were even murdered. Also, cases occur when a first mate would kill the captain to take over.