What pirate ship first used the skull and crossbones?

Emanuel [Emmanuel] Wynn [Wynne]'s ship.
(alternative spellings)

1) "Black flags are known to have been used by pirates at least five years before the earliest known attachment of the name "Jolly Roger" to such flags. Contemporary accounts show Captain Martel's pirates using a black flag in 1716, Edward Teach, Charles Vane, and Richard Worley in 1718, and Howell Davis in 1719.

An even earlier use of a black flag with skull, crossbones, and hourglass is attributed in 1700 to pirate captain Emanuel Wynn, according to a wide variety of secondary sources. Reportedly, these secondary sources are based on the account of Captain John Cranby of the HMS Poole and are verified at the London Public Record Office."
Source and further information:
http://en.wikipedia.org/wiki/Jolly_Roger


2) "Emanuel Wynn (or Emanuel Wynne) was a French pirate of the 1700s, and was the first pirate to fly the Jolly Roger. His design incorporated an hourglass beneath the bones to represent that time was running out.

British Admiralty Records, in the Public Records Office in the UK show, in a report dated 18 July 1700, that HMS Poole, commanded by Captain John Cranby, engaged Wynn's ship off the Cape Verde islands. Cranby chased Wynn into a cove at Brava Island but, assisted by Portuguese soldiers, Wynn escaped Poole. Most historians agree that Cranby's account is the first mention of a Jolly Roger, which Cranby described as "a sable ensign with cross bones, a death's head, and an hour glass." Wynne is believed to be the first (or some sources contend one of the first) pirate to fly the now familiar form of the jolly roger. His flag, showing the distinctive skull and crossbones motif, was augmented with another common pirate symbol: an hourglass (meant to signify to his prey that only by timely surrender could they evade death).

Wynne began his piratical career raiding English merchantmen off the coast of the Province of Carolina near the end of the 17th century. He later moved to the more profitable waters of the Caribbean, attacking both English and Spanish ships."
Source and further information:
http://en.wikipedia.org/wiki/Emanuel_Wynn

Further information:
http://www.bonaventure.org.uk/ed/flags.htm

Henry Avery, or Every had one in the 1690s.the ship was called the "Fancy" by Every,having originally been the "Charles" I think. The final resting place of the "Fancy" oddly enough was New Providence,which years later would be the epicenter of piracy in the Americas. I've seen Every's flag with both a black background and a red one in accounts and history on pirates.

This design was used by four pirates, captains Edward England, John Taylor, Sam Bellamy and John Martel.

- Wikipedia
http://en.wikipedia.org/wiki/Jolly_Roger

i thought you were looking for the pirates name, guess i did answer your question then. "Jolly Roger"

i dont know which pirate it was, but i am fairly sure he sailed "the jolly roger". look that up and see.