A Commanding Officer (or CO) is the highest ranking officer and commander of a unit. On starships, the CO has the rank of captain or even a commander grade. On starbases, the CO could be an admiral grade, a captain, or a commander grade.
On starships, it is general practice to address the commanding officer as "Captain," regardless of their actual rank. (DS9: "Behind the Lines")
In general, commanding officers are always dressed in the colors of the command division but there are sometimes exceptions in Starfleet uniform usage.