Admiral Wilson's Royal Navy was fresh from the exploits of Collingwood and Nelson. There was no room in it for a damned un-English weapon like a submarine. With his words in mind, Lieutenant Commander (later Admiral Sir) Max Kennedy Horton flew the first Jolly Roger in 1914, from HMS E9, on return to harbour after sinking the German cruiser SMS HELA and the destroyer S-116. It was undoubtedly a result of Admiral Wilson's comment of 13 years previously and was probably intended as grim humour.
Initially, a new flag was flown (adding to any existing ones) each time the submarine returned from patrol, but this soon became unwieldy. A larger Jolly Roger was eventually made and symbols added representing E9's exploits. Other submarines soon adopted the practice but it didn't really become popular until World War Two.
The first Jolly Roger of that war was the one presented to the First Flotilla at Alexandria, Egypt, some time in early 1941. From there the practice spread to Malta, where Lieutenant Commander Malcom Wanklyn was so successful in the original HMS UPHOLDER, and then to the home flotillas. It also didn't take long for this custom to spread to other Allied navies.
Like most successful traditions, there are rules governing its use. It cannot be flown until the submarine has scored its first success, and then only for the day the boat returns to harbour. It may also be flown, however, on the day the submarine returns to home port after a foreign commission.
The image to the left is the first known photo of a Jolly Roger. It is being flown from the main periscope of the Vickers Canada, Montreal-built submarine HMS H5 on returning to Great Yarmouth after sinking U-51 on 14 July 1916. The boat was commanded by Lt Cromwell H. Varley, RN, and the officer in the photo is Lt John Byron, RNR, the Navigator.
Different symbols are attached to the main flag to indicate what sort of successes the boat has had:
A white bar indicates a merchant ship has been torpedoed.
A red bar indicates a warship has been torpedoed.
Indicates a submarine has been torpedoed.
Indicates a damaged warship.
Crossed gun barrels with a white star - merchant ship sunk by gunfire. With a red star - warship sunk by gunfire. Each action rates one star only, even if multiple ships are sunk at the same time.
Small ship sunk by gunfire.
Very small ship sunk by gunfire. The chamber pot is a reference to submariners slang for barely worthwhile targets.
Minelaying operations. Sometimes the number of mines are indicated as well.
Aircraft shot down.
Train or railway track destroyed by gunfire.
Special operations - cloak and dagger work like dropping or picking up agents on enemy shores. To indicate such a mission, most submarines used a dagger, however the original HMS UNSEEN was allowed to use the symbol of 'The Saint' books by special permission of the author, Leslie Charteris. The number of halos indicated the number of special operations missions completed.
Chariot operations. Chariots were also known as 'jeeps' and this character, famous for saying 'jeep-jeep' is for a WW2-era cartoon.
Air-sea rescue.
Submarine exceeded deep diving depth.
Demolition ops.
Beach marking ops.
This image is the Jolly Roger from the original HMS UNSEEN. This photograph was taken at Digby, Nova Scotia in 1944. Notice the use of the symbol from The Saint series of books.