In Treasure Island, the first pirate to receive a "black spot" is Billy Bones. Blind Pew gives him the spot as a sign that he must share the treasure map with the other pirates, on pain of death. Later, Long John Silver receives a black spot, meaning that he is to be deposed as leader of the pirates. In both cases, the black spot is a threat of death, warning the pirate in question that he must comply with the judgment of his shipmates and that failure to do so will be dangerous.
The black spot appears to be an invention of Stevenson's, though he may have gotten the idea from a tradition that pirates used the Ace of Spades from a pack of playing cards to identify a traitor. Although the black spot usually had a specific message written on the other side, the symbol itself was of primary importance, and the pirate would not need to read the message to know what it meant. This made the black spot more effective than a letter or note, as many pirates would have been illiterate, or nearly so. In addition to this, the black spot, like the Jolly Roger and other images associated with piracy, is a menacing symbol in itself.