It is sometimes claimed that the term derives from 'Joli Rouge' ('Pretty Red') in reference to a red flag used by French privateers. This description closely resembles the flags of a number of Golden Age pirates. Richard Hawkins, who was captured by pirates in 1724, reported that the pirates had a black flag bearing the figure of a skeleton stabbing a heart with a spear, which they named 'Jolly Roger'.

Neither Spriggs' nor Roberts' Jolly Roger consisted of a skull and crossbones. While Spriggs and Roberts used the same name for their flags, their flag designs were very different, suggesting that already 'Jolly Roger' was a generic term for black pirate flags rather than a name for any single specific design. Johnson specifically cites two pirates as having named their flag 'Jolly Roger': Bartholomew Roberts in June 1721 and Francis Spriggs in December 1723. Use of the term Jolly Roger in reference to pirate flags goes back to at least Charles Johnson's A General History of the Pyrates, published in Britain in 1724. It became the most commonly used pirate flag during the 1720s, although other designs were also in use. The flag most commonly identified as the Jolly Roger today – the skull and crossbones symbol on a black flag – was used during the 1710s by a number of pirate captains, including Black Sam Bellamy, Edward England, and John Taylor. Jolly Roger is the traditional English name for the flags flown to identify a pirate ship preceding or during an attack, during the early 18th century (the latter part of the Golden Age of Piracy). The pirate captain Jean Thomas Dulaien would wait for the enemy to fire three or more cannon shots after raising the red flag before giving the order to attack with no quarter given. Followed by warning shots, if the enemy did not strike their own flag to signal surrender, the red flag (or bloody flag as it is known) was raised, signaling that the target's cargo/valuables will be taken by force and that ' no quarter' will be given if the enemy ship continued to refuse surrender. After closing in on a target ship, the black flag would be raised, signaling that ' quarter' will be given if the target crew surrendered their cargo/valuables without a fight. The black flag was part of a flag signal combo, together with a plain red flag. Prior to the advent and popularization of the 'Jolly Roger' we know today, western pirates flew a simple black flag, initially devoid of design.

Pirate plague of the dead