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United Kingdom: Royal Naval Submarine Service

Use of Jolly Roger by submarine service

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Use of Jolly Roger by submarine service

A Jolly Roger flag, but defaced by a number of varying symbols dependent upon the type of action and used unofficially by the submarine service of the British Royal Navy to signify that the boat flying it had engaged an enemy (see also 'defaced').

It should be further noted that a torpedo attack which resulted in an enemy vessel being sunk was symbolized by a bar or torpedo, with the number of successful attacks matched by the number of symbols. A successful gun engagement was shown by a pair of cross cannons and an enemy plane downed by the silhouette of an aircraft, with each occurrence being represented by a star. Assistance in a clandestine operation (the landing of agents or commandos) was marked by the display of a dagger, with any further such operations calling for either stars or more daggers.
Christopher Southworth, 22 February

I've come across a fuller list of these defacements, that I copied down from the displays at the RN Submarine Museum at Gosport a few years ago:

red bar: enemy surface vessel sunk
red bar with a U superimposed: enemy submarine sunk
white bar: enemy merchant vessel sunk
yellow bar: Japanese merchant vessel sunk
crossed guns and a star: enemy vessel sunk by gunfire
a chevron: small enemy vessel sunk by gunfire
a chamber pot or a Chinese junk: very small enemy vessel sunk by gunfire
a lighthouse and torch: participation in an amphibious operation (the torch on its own is often used for participation of Operation 'Torch', the landings in North Africa in 1942)
a lifebelt: air-sea rescue operation
a dagger, sword or 'The Saint' stick figure (from the novels of Leslie Charteris): landing agents or commandos ('cloak and dagger' operations in the slang of the time)
a 'jeep' (character in Popeye cartoons): chariot recovery (a 'chariot' was a one- or two-man submersible, used for raids on the shipping in enemy harbours)
a railway engine: train or track destroyed
a demolition charge: ship sunk (the difference between this and the bars above for sunken vessels was not made clear)
diver's helmet: going below safe diving depth
a tin opener: used by HM S/M Proteus after an Italian torpedo boat passing overhead collided with the submarine, and ripped open the submarine's ballast tanks
a mine: mine-laying operations
a cross patee: supply runs to Malta during the siege of 1942
an aircraft: enemy aircraft shot down
a red flower: minefield reconnaissance

The flags themselves were always unofficial, which accounts for the different symbols for the same kind of operation, or the symbols which were used only by one boat, like the tin opener (or the stork and baby flag flown on one occasion by HM S/M United after a mission of mercy).
Ian Sumner, 23 February 2007

Some further symbols:

crossed sabres - boardings
dog - operation "Husky" (invasion on Sicily 1943)
grating - forced net barrier

Grzegorz Skrukwa, 15 April 2002