Jolly Roger became the generic term when referring to a pirate flag. The term likely came out of twisting the French joli rouge which meant pretty red. The early buccaneers flew red banners and flags to strike fear in the others they encountered.
English pirate Henry Every also known as John Avery may have been one of the first to transition to the iconic pirate flag with the skull and cross bones. His years of piracy spanned 1694 to 1696 and he is reported to have flown two different flags. He originally flew a traditional red flag with chevrons but later switched to a black flag with a skull in profile above cross bones. Whether he actually switched to the second flag is still up for debate.
French pirate Emanuel Wynne is given confirmed credit as the first to use the skull and cross bones. Captain John Cranby of the British naval ship HMS Poole entered into official record in 1700 an encounter with Wynne and his ship which flew a black flag with a skull that appeared to rest on cross bones as an hourglass was below it. The hourglass was a common pirate symbol which told they opposition they should surrender in a timely manner.
English pirate Richard Worley simplified his flag to just the skull resting on the crossbones on a black flag. His piracy career only lasted September 1718 to February 1719. His short career ended after his capture and execution.
Irish pirate Edward England who was born as Edward Seeger created what is considered the classic pirate flag with the skull above the cross bones on a black flag. His piracy career spanned from 1717 to 1720. The character Long John Silver was patterned after England by Robert Louis Stevenson.