The black spot is another of Robert Louis Stevenson's wonderful literary inventions, and it has been an integral part of pirate and criminal folklore ever since. In Treasure Island, although the pirates are a bunch of bloodthirsty criminals, they do still live by a kind of code. This code is not always successful, greed for loot and treasure often gets in the way, but for the most part, they stick to the old pirate ways.
One of the time-honored pirate traditions is the black spot. The idea is that when a captain is about to be deposed, he is given a slip of paper with a black spot on it. This is the pirate equivalent of a judgement in a court of law. When a captain receives this piece of paper, he knows that he has violated the pirate code and must be punished accordingly.
Long John Silver's crew have the audacity to present him with the black spot. But Silver has been at this game too long to be spooked by it. The black spot given to the old sea dog has been painted on a page crudely torn from a Bible. Like most seamen of the time, the pirates in Treasure Island are deeply superstitious, and painting a black spot on a page from the Bible is considered bad luck. As a result, Silver knows that he really has nothing to fear from his men.