There were a variety of flags flown by ships of the Commonwealth of England and the Commonwealth of England, Scotland and Ireland during the period of Interregnum of 1649-1660.
At sea, royalist ships continued to fly the Union Jack of 1606, while the parliamentary navy on 22 February 1649 was ordered by the Council of State (signed by Oliver Cromwell on 23 February) "that the ships at sea in service of the State shall onely beare the red Crosse in a white flag" (viz., the flag of England). On 5 March 1649 the Council ordered "that the Flagg that is to be borne by the Admiral, Vice-Admiral, and Rere-Admiral be that now presented, viz., the Armes of England and Ireland in two severall Escotcheons in a Red Flagg, within a compartment." A sole surviving example of a naval flag following this description is kept by the National Maritime Museum, Greenwich, all others falling victim to the destruction of Commonwealth symbols at the Restoration of Charles II. Scotland was formally reunited with England in 1654. According to Perrin (1922), the saltire of Scotland did not reappear on naval flags until 1658.
Cromwell's personal standard as Lord Protector became the 'Standard for the General of his Highnesse fleet' in 1658, while the Cross-and-Harp jack was replaced by the "Protectorate Jack", consisting of the old Union Jack with the addition of the Irish Harp at the center.