Master was originally 'sailing master', a warrant officer in charge of ship handling and navigation. Captains were 'gentlemen' who didn't need to know about such things. This would be in the 17th century, but gradually captains who were fully competent in ship handling and navigation became the norm.

Smaller vessels (between 14 and 18 guns, normally referred to as sloops) were commanded by a Master and Commander (Master Commandant in the US Navy) who was expected to act as his own sailing master. By about 1770 sailing masters were appointed to these vessels also, and gradually Masters and Commanders were just referred to as Commander, the present rank.

Masters were 'warrant officers of wardroom rank' and so messed with the lieutenants but were junior in rank. The other 'warrant officers of wardroom rank' were the surgeon, purser and chaplain. The master would also have a number of 'master's mates' who messed in the gunroom with the midshipmen but were senior to them.

The above refers to national navies. Mercantile practice was different, but, for instance, East Indiamen would have a Captain and a Sailing Master, and the man in charge of a much smaller vessel would be more likely to be referred to as the Master of such-a-vessel than the Captain. This again changed over time. Captain was a jealously guarded title and the master of of a very small vessel who called himself 'Captain' would have been considered to be putting on airs.

The above refers to Navies