Captain: A ship’s captain is usually an experienced sailor, navigator, and commander. There is a good deal of overlap between captain and master; generally, a master is someone who owns the ship she commands, while a captain is someone who does not. A ship might sail with both a captain and a master, in which case the master generally permits the captain to exercise command and only intercedes if she feels her vessel is at risk.
A captain is usually an expert (or multiclass expert), bard, fighter, paladin, or rogue with at least 7 to 10 ranks in Profession (sailor), 4 to 7 ranks in Knowledge (geography), 2 to 4 ranks in Knowledge (nature) or Survival, and 2 to 4 ranks in an interaction skill such as Bluff, Diplomacy, or Intimidate.
Master: The term master can overlap with the term captain in some degree. In general, a master owns her vessel, while a captain doesn’t but typically exercises complete authority over all matters of sailing, navigation, discipline, and administration of the crew.
A master is usually an expert (or multiclass expert) or rogue with at least 7 to 10 ranks in Profession (sailor), 4 to 7 ranks in Knowledge (geography), 2 to 4 ranks in Knowledge (nature) or Survival, 2 to 4 ranks in an interaction skill such as Bluff, Diplomacy, or Intimidate, and 2 to 4 ranks in Profession (merchant).