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Recently I have been digging on the internet for information on the ensigns worn by various types of British and Commonwealth vessels, and I thought I would share my findings here in case someone is interested.

• Commonwealth merchant vessels
  Looking into Lloyd's records of merchant ships owned by Commonwealth steamship companies, I was surprised to discover that all of them were registered as British-flagged ones, no matter if their companies were actually based in the UK or not.
  
  The 2,053-ton bulk carrier Magog, for example, was owned by Canada Steamship Lines, a Montreal-based shipping company. As expected, uboat.net reports the ship as Canadian but convoyweb.org and, more importantly, the 1939 Lloyd Register have her as British. I have checked many other Canadian, Australian, New Zealand, etc. vessels, and they all were registered as British. As far as I can see there are two possible explaination to that:
  
  
  1. all the merchant vessels of the Commonwealth wore the Red Ensign;
     
     
  2. vessels belonging to (former) British colonies wore the Red Ensign (optionally) defaced with each country's national emblem, but Red Ensign variants were still officially considered (and registered) as British flags.
  
  In order to investigate the veracity of the last point I have checked many photographs. Discernig small flag details based on pictures which usually have a poor resolution is not so easy, nonetheless I think I have found a few photographs which seem to confirm my hypothesis.
  
  
   

  
  The picture above and the one below portray the Morialta and the Ulooloo respectively, both owned by Adelaide Steamship Company
  
  
   

  
  Both vessels have a Red Ensign hoisted on the flagstaff. The Union Jack on flag's canton is easily discernible, but can you see the white spot beneath it? Well, I am not 100% sure, but that might be one of the stars defacing the Australian Red Ensign
  
  One last picture, this time of the Princess Marguerite, a passenger ferry managed by British Columbia Coast Steamships, a division of the Montreal-based Canadian Pacific Railway Company
  
  
   

  
  Again, a brighter spot is barely discernible; that migh be the bottom portion of the coat of arms defacing the Canadian Red Ensign
  
  
• Catapult Aircraft Merchant ships/Merchant Aircraft Carriers
  Those were merchant vessels, owned by the Ministry of War Transport but managed by private companies and commanded/crewed by civils, threfore the regular civil (red) ensign was flown aboard them.
  
  
• Armed Merchant Cruisers
  They were merchant ships requisitioned by the Admiralty and commissioned in the Royal Navy for convoy defense. They were given the HMS prefix and, as any other naval vessel, they wore the White Ensign.
  
  
• Royal Fleet Auxiliary ships
  Mostly oilers, depot ships, fleet tenders, etc, either purpose-built or requisitioned for that purpose. They were commanded and crewed by members of the Royal Naval Reserve, they were given the RFA prefix and they wore the Admiralty Blue Ensign (former Transport Ensign): a Blue Ensign defaced with a horizontal yellow anchor.
  
  Source: http://www.historicalrfa.org/archive...ign-of-the-rfa
  
  
• Q-ships
  Basically heavily armed AMCs in disguise.
  
  

  In 1939 Winston Churchill gave authority for a number of merchantmen to be requisitioned for service as Q-ships, although for security purposes they were referred to as Special service Freighters. A fleet of nine small mainly coal-burning vessels were acquired , six for deep-sea work and three for coastal work. All were commissioned as HM ships under their original names but were given RFA cover names and on entering harbour and while in harbour they wore the Blue Ensign, behaved as RFA’s and adopted the RFA commercial practices. None of them was really suitable for their intended roles and met with a complete lack of success. Their Q-ship service officially ended on 2 March 1941

  Source: http://www.historicalrfa.org/rfa-cha...ip-information
  
  
• Royal Mail Ships
  A number o merchant vessels, especially ferries and ocean liners, were given the RMS prefix and designated to carry mail under contract to the British Royal Mail.
  The Flags of the Word project lists a Royal Mail Blue Ensign and the National Maritime Museum of Greenwich has one of these ensigns in its collection. Apparently this flag was worn by RM ships after 1902, but I ignore wether it was still in use at the oneset of WWII, when most RM ships were requisitioned as troop transports and swithched to other flags.
  
  
• Hospital Ships
  During WWII the Ministry of War requsitioned a number of private-owned ocean liners for use as hospital ships. The appearance of those vessels was regulated by the Hague Convention of 1907 and subsequent international agreements.
  
  

  It had long been acknowledged that the system of marking hospital ships adopted in 1907, at a time when air forces did not exist, was completely inadequate. Hospital ships were to be painted white outside with a horizontal band of green or red, and were to fly the red cross flag. The experts who met in 1937 recommended that large red crosses on a white ground should be painted on the hull and deck of hospital ships. During the Second World War, the belligerents often adopted that means of identification. It is clear from the records that the lack of an up-to-date system of marking, visible at a great distance, was the cause of most of the attacks made on hospital ships during the Second World War.
  
  [...]
  
  The national flag of the belligerent must be flown. On the other hand, a hospital ship will not fly the pennant hoisted by warships.
  Hospital ships belonging to a neutral State and assisting a belligerent must fly their national flag as well as that of the belligerent concerned. The records of the 1907 Conference at The Hague indicate where the flags should be flown: the flag of the neutral State is to be flown in its usual place, and the flag of the belligerent together with the red cross flag is to be flown from the mainmast.
  Last and most important, hospital ships must fly a white flag with a red cross. That provision already existed in the earlier instruments, but the 1949 Diplomatic Conference decided to specify where it should be flown, although that place had already become traditional as may be seen from the reference above: it is to be flown at the mainmast, as high as possible. Why should this be so? Because it is the part of the ship which first appears over the horizon. The white flag with a red cross will therefore be placed above the flag of the belligerent.

  source: https://ihl-databases.icrc.org/ihl/0...2563cd00424636
  
  Summing up, the general rule for hospital ships was to fly their national ensign "in its usual place" (i.e. at ship's stern while underway) + red cross flag on the mainmast "as high as possible" + the national ensign of the concerned belligerent if the ship belonged to a neutral country.
  
  Now the matter is: which was the ensign used aboard Commonwealth hospital ships? The following document (p. 7, fig. 9), gives a contradictory answer:
  
  https://maritimearchaeologytrust.org...-Burns_WEB.pdf
  
  The flag shown in fig. 9, p. 7 is a Board of Trade Blue Ensign, yet the caption reads: HMHS Lady Connaught Flag: “A Blue Ensign Flat”.
  
  A thread on Great War Forum sheds some light on the issue:
  
  

  A recent thread about the correct prefix for hospital ships ventured into some interesting byways which included debate about the ensign flown by hospital ships. It was pointed out that hospital ships were not commissioned into the Royal Navy and therefore would not have flown the white ensign, and that all warrants to fly the plain blue ensign were cancelled in August 1914, so the choice was between the red ensign and a blue ensign defaced with a horizontal anchor, sometimes known as the Admiralty Ensign. For anyone interested in this debate, I have just come across a 1917 HMSO pamphlet entitled 'Correspondence with the German Government regarding the Alleged Misuse of British Hospital Ships' which, as well as being an interesting read, seems to resolve the ensign question.
  
  The pamphlet contains memoranda from the German Government (delivered via United States embassies) documenting the allegations of misuse and advising Britain that it intends as a consequence to treat as belligerent any hospital ship encountered in the southern North Sea, the English Channel and parts of the Mediterranean. The pamphlet also contains the British Government's detailed rebuttals to each of the allegations. One of these contains the sentence (p 12), 'All British hospital ships have their names painted distinctly on them in the usual place, and all fly the Red Cross flag and the British defaced Blue Ensign worn by transports.'

  The text above is relative to WWI, nonetheless a similar restriction to the one of 1914 was issued in 1939 ("All Blue Ensign warrants were cancelled in 1939"), so it is unlikely for Britsh hospital ships of WWII to have flown the "Blue Ensign flat". Instead of that, the probably following the WWI usage of the Transport Ensign, or they might have switched to the Board of Trade Ensign.
  
  
  Infantry landing ships
  According to Wikipedia (mentioning as reference: Bruce, Colin J. Invaders, Chatham Publishing, London, 1999 ):
  
  

  Some of the LSIs were commissioned into the Royal Navy, received navy crews, and flew the White Ensign, while most retained their civilian crews and flew the Red Ensign.

• Troop transports
  Here I wish we had more information. The one source I have found so far is a comprehensive study on British ensigns published in 2015
  
  Among the other flags, it mentions (at p. 29):
  
  

  Department for Business, Enterprise and Regulatory Reform Circular Picture of Three Masted Ship at Sea. Available for use on land, and on any vessels that the department might operate. It was originally the Board of Trade ensign, and has had a variety of uses. In the 1920s troopships carrying army or air force personnel flew it and in the 1960s UK Trade Commissions used it as a car flag.

  Whether the usage of the Board of Trade Blue Ensign started in the 20's lasted until WWII or not is a mystery to me, but it is likely that, similar to infantry landing ships, some troopers manned by civilian crews might have flown the Red Ensign.
  

Summary of the flags mentioned in this post and their usage:

Merchant vessels / Some troop transports (?) / Some Landing Ships / CAM/MAC ships
British Red Ensign *

As above
Australian Red Ensign

As above
Canadian Red Ensign

As above
New Zealand Red Ensign

As above
South African Red Ensign **

Royal Mail Ships (?)
Royal Mail Ensign

Royal Fleet Auxiliary vessels / Q-ships / Hospital Ships (?)
Admiralty, Government
Service or Transport Ensign

Troop Transports (?) / Hospital Ships (?)
Board of Trade Ensign

Vessels commissioned in one of the Commonwealth navies (ilcuding some landing ships), except Q-ships
White Ensign

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Notes

* The Red Ensign (undefaced) was also the civil ensign flown aboard merchant vessels registered in British India. While the Raj had its own version of the Red Ensign defaced with the so called "star of India", this flag had only a limited use:

No Admiralty Warrant was issued for this ensign which was an unofficial, or semi-official land flag. It was used between 1945 and 1947 in the context of India's membership of the United Nations, and possibly used earlier to denote India's membership of the League of Nations.

Source: Flags of the World

[...] the Red Ensign was used as the civil ensign and sometimes represented India in international events, notably in the Declaration by United Nations during World War II. The ensign used on merchant ships registered in British Indian ports was the undefaced red ensign.

Source: Wikipedia (see link above)

** Since 1928 South Africa had its own national flag, nonetheless...

The South African "Red Ensign" used unofficially as a de facto national flag until 1928 [...] continued being used sparsely in limited contexts until the early 1950s.

source: Wikipedia (see link above)

Even after the Union adopted the new national flag in 1928, it continued to use the South African Red Ensign in its proper role as the Merchant Marine ensign until 1951 before the Merchant Shipping Act of that year designated the orange-white-blue national flag also as the Merchant ensign.

The Red Ensign was for use at sea as the merchant fleet ensign. This version of the South African Red Ensign continued in use in the merchant navy until 1951 when it was finally displaced at sea by the South African national flag in terms of the Merchant Shipping Act of that year.

Various sources inform us that the Red Ensign with South African flag badge was replaced by the South African national flag as the merchant ensign in 1951, and some writers state that this was in terms of the Merchant Shipping Act 1951. Well, section 65 of this Act, in its original form, did indeed state that "the national flag of the Union is hereby declared to be the national colours for all ships registered in the Union" -- but the Act wasn't brought into operation in 1951. It was kept in abeyance for several years.

Source: Flags of the World

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That should be all for now guys. In case you find any wrong information, if you think I have missed some notable flag or vessel type, or if you can provide new information relevant to the subject of this post, I will gladly update it with your imputs