Many people associate a black flag featuring a skull and crossbones design with pirates, and many use the term “Jolly Roger” to refer to such a flag. Given that the pirate flag is not terribly jolly and it does not seem to involve anyone named Roger, many people wonder what the origins of the name are. As is often the case with popular folk terms, the meaning behind the Jolly Roger is somewhat obscure and uncertain, although several hypotheses for the name have been put forward.
Pirates have been plying the seas for centuries, typically attempting to capture ships with their crew and cargo intact. Many early pirates actually ran quite democratic ships, encouraging the crews of captured ships to join forces and merely imprisoning those who resisted until the next port of call. Pirates used flags to communicate their intentions to other ships, typically flying false colors until they got close enough to capture a ship. The Jolly Roger was flown to encourage a ship to surrender.
Pirates typically flew black flags, with a red flag indicating that the pirates would give no quarter to resisters. The use of bones on pirate flags dates back to at least the 1600s, and possibly earlier. Many cultures associate potent symbolism with bones, which are meant to remind people of their own mortality and failings. Numerous variations on the skull and crossbones designs were used by pirates, and by 1720s, several accounts referred to pirate flags as “Jolly Rogers.”
One theory behind the name is that it may be a corruption of the French jolie rouge, for “pretty red,” in a reference to the red flags flown by some pirates. However, historians do not see much evidence for the use of jolie rouge in reference to a pirate flag. Some theorists have also suggested that it may be an Anglicization of “Ali Raja,” an infamous Tamil pirate who terrorized the seas and presumably flew a black flag as well. Both of these folk etymologies derive the meaning of "Jolly Roger" backward, trying to come up with old terms which could have been transmuted into a modern phrase.
Although both of these explanations are colorful, the real origins are probably more mundane. In England, “Roger” is closely related to “rogue,” and many people refer to the devil as Old Roger, or say that they are “rogering” someone when they are making trouble for them. Since pirates are associated with roguish behavior, naming their flag the Jolly Roger would have made sense, since rogues tend to be particularly jolly when they are making mischief, as pirates often are.