From Hidden Frontier
A commanding officer (or CO) is a term used to describe one's rank in relation to others within the same environment.
One meaning of commanding officer is the highest-ranking officer and commander of a unit. On starships, the CO usually has the rank of Captain, though sometimes a Commodore or Fleet Captain may also hold this position. Depending on the size, mission and circumstance of a vessel, officers of lower rank can also serve as a commanding officer. The officer in command of a vessel, regardless of rank or size of the ship in question, is typically referred to as "Captain".