In order to install fear into the hearts of the ships that the Pirates were about to attack, the pirates would hoist up the Jolly Rodger to show their victims just who they were dealing with.
Here are some real pirate Jolly Rogers from history:

Emanuel Wynn

Emanuel Wynn's Jolly Roger

Back in 1700, Wynne is believed to be the first pirate to fly the now familiar form of the jolly roger. His flag, showing the distinctive skull and crossbones motif, also had another common pirate symbol: an hourglass (meant to signify to his prey that only by timely surrender could they evade death).

Calico Jack (John Rackham)

Calico Jack's Jolly Roger

Calico Jack's flag showed a skull over crossed cutlasses. In spite of the fact that other pirates were more successful, his flag has gained fame as "the" pirate flag.

Henry Avery ("Long Ben")

Henry Avery's Jolly Roger

Avery's flag showed a skull wearing a kerchief in profile over crossbones.

Black Bart (Bartholomew Rogers)

Black Bart's Jolly Roger #1

Black Bart used several flags during this time. The one usually associated with him was black with a white skeleton and white pirate holding an hourglass between them: it meant that time was running out for his victims.

Black Bart (Bartholomew Rogers) Second Flag

Black Bart's Jolly Roger #2

Black Bart hated the islands of Barbados and Martinique, so made a special flag to make his point: a black flag with a white pirate standing on two skulls. Underneath were the white letters ABH and AMH. This stood for "A Barbadian's Head" and "A Martinico's Head."


Blackbeard's Jolly Roger

His flag showed a skeleton with horns holding an spear in one hand and hourglass in the other that is pointing to a heart dripping three blood drops.

Edward Low

Edward Low's Jolly Roger

His flag was black with a red skeleton.

John Quelch

John Quelch's Jolly Roger

Some say that John Quelch flew a pirate flag referred to as Old Roger by his crew. Some people think this might be the origin of the name Jolly Roger. It is alleged that his theme was later borrowed by Blackbeard and also Bartholomew "Black Bart" Roberts.

Stede Bonnet

Stede Bonnet's Jolly Roger

Bonnet's flag was black with a white skull over a bone in the middle: on either side of the skull were a dagger and a heart.

Thomas Tew

Thomas Tew's Jolly Roger

Tew’s flag is said to have been a white arm holding a sword on a black background, this probably meant "we are ready to kill you.”

Walter Kennedy

Walter Kennedy's Jolly Roger

Walter Kennedy's Jolly Roger was identical to the flag of French Pirate Jean Thomas Dulaien.