Thankfully, there's Eagle Vision. Clicking the left analog stick allows hero Edward Kenway to get a much better view of his surroundings using a filter of sorts that separates innocent civilians from bad guys.
While viewing the world using Eagle Vision, keep in mind that enemies are red, objectives are gold, allies are blue and everyone else has no hue at all. Meanwhile, points of interest (think Stalking Zones) possess a white glow.
Eagle Vision appeared in previous Assassin's Creed games, but in Black Flag, the game marks hostiles and persons of interest, allowing you to see these people through solid objects. Remember that you lose this ability whenever Edward moves 35 meters away from his target(s).