The Submarine Service -- one of the fighting arms of the Royal Navy -- is sometimes known as the Silent Service and, although usually effective, it has not always been popular amongst more traditional British officers. Admiral Sir Arthur Wilson (UK First Sea Lord, 1910-1911) complained that submarines were "underhanded, unfair, and damned un-English" and that the personnel should be hanged as pirates.

In reaction to this attitude, during World War I Lieutenant Commander Max Horton began flying the Jolly Roger – the white-on-black pirate flag -- when his submarine returned from successful patrols. The practice developed to flying an adapted skull-and-crossbones flag, on to which symbols indicating the submarine's achievements were sewn. The practice of flying the Jolly Roger was adopted by other submarines during World War I and became more widespread in World War II.

Flying the Jolly Roger has continued into modern times. There was a stir in the media when HMS “Conqueror” raised the flag on return to Faslane (Scotland) in July 1982. This was in recognition of the successful attack on the Argentine cruiser ARA “General Belgrano” during the Falklands War. This Jolly Roger, now displayed in the Royal Navy Submarine Museum, featured an atom to mark HMS “Conqueror” as the only nuclear submarine with a kill, crossed torpedoes for the type of weapon used, a dagger indicating a cloak-and-dagger operation, and the outline of a cruiser for the kind of ship that had been sunk.

More Info: en.wikipedia.org