This, like parrots, planks and eye patches, is one of the famous accouterments of pirate life, or in this case, death. When a pirate had done something truly awful, and usually, done several things truly awful, and usually, several truly awful things, pretty often to many of his friends, he was given a death sentence. The mark of this sentence was a black spot of ink on a page ripped from the bible. It informed the soon to be deceased that his time had come.
From Treasure Island to Pirates of the Caribbean The Black Spot is a staple of Pirate movies and stories.