| 1 Commonwealth Ensign 1649 |
| 2 Cromwell's "Great Union" 1658 |
| 3 Ensign Red—Charles II.—1660 |
It was to take the place of the King's Standard at the stern that the Commonwealth Parliament created a flag, called the Commonwealth Ensign (Pl. [IV.], fig. 1), to be carried on their men-of-war. This was a red flag, having in the fly a yellow Irish harp, and in the upper corner next the staff the St. George cross upon a white ground. Ireland had early been overrun by the Commonwealth armies, so her emblem was included in the flag, but Scotland had warmly espoused the cause of the Stuarts, and was, therefore, not recognized.
Cromwell, after he had been raised to the position of Protector, and had dragooned Scotland into submission, put out, in 1658, another flag as the "Great Union," or banner of the Commonwealth (Pl. [IV.] , fig. 2), in which the crosses of St. George and St. Andrew were shown for England and Scotland, and the harp, on a blue ground, for Ireland; but they were each placed in separate quarters of the flag, instead of being joined together in one union, and on a black shield in the centre he caused to be displayed a lion rampant, as representing his own coat-of-arms and himself.
This "Great Union" of Cromwell does not appear to have entered into much use, although it certainly was displayed at his funeral.
The fleets of the navy were then flying ensigns of three different colours—red, blue and white—according to the rank of the admirals who were in command, red being the colour of the admirals of highest rank and the typical colour of England.[46]
Contemporary paintings also show that red, blue and white ensigns were in use under the Commonwealth, with a single harp in the fly, and a Dutch medal, struck to commemorate the death of Admiral Tromp, also shows the same design of flag.
The "Commonwealth Ensign," now having the Irish harp inserted in the flag, was the official flag flown at the stern of the ships of the States Navy during the period of the Commonwealth.
The rule of the Commonwealth party having, shortly after the death of Cromwell, come to its sudden termination, the Royalist supporters of the absent King did not take time or wait for any formal proclamation authorizing a change in flags which had come into existence under the order of the Commonwealth Council.
Pepys tells in his "Diary" of how this change was begun. Being "Clerk of the Acts of the Navy," he had been deputed to read the proclamation of Parliament declaring the restoration of the King to the crews on board those ships of the Navy which had been appointed to cross over to The Hague and bring Charles II. to England.
Under the Commonwealth successful generals and officers on land had been appointed to commands as admirals and officers in the navy, and the military titles were still retained, the official title of the officers in highest command in the navy of the Commonwealth being "Admirals and Generals at Sea."