Colonel John Fitzgerald was an experienced officer who had commanded an Irish Regiment in the service of Charles II in exile in the Low Countries, and commanded it at the battle of the Dunes in 1658. Pepys records that Fitzgerald was a great favourite of the Duke of York, who wished to promote him, but Norwood, Bridge, and Peterborough were all hostile and so the Privy Council blocked his preferment. His regiment had joined the Dunkirk garrison after the Restoration on 12th March 1661, and he sailed with his regiment and the regiment of Farrell for Tangier in January 1662.

In April 1663 Andrew Rutherford, Earl of Teviot, the Governor of Tangier, was ordered to reduce the two Irish regiments in the garrison to one of five companies, under Fitzgerald’s command. On 4th May 1664, Teviot was killed in a Moorish ambush. Fitzgerald was then on leave and was instructed to return immediately. This he did and was appointed Governor, and thereby Colonel of the Governor’s Regiment, on 7th June 1664. He was at the same time instructed to reorganise the two Regiments into two of roughly equal size, eliminating the national differences. This was done for two reasons. First to spread the veterans of good fighting quality around and stiffen the rest, secondly to eliminate a dangerous degree of Republicanism present among the soldiery of the English Regiment - who were in great part former Protectorate men. Interestingly, it was Norwood who was to command the Lieutenant Governor’s Regiment.

On the arrival of Bellasise as Governor, the Commission Register still shows Fitzgerald as Colonel of the Governor’s regiment, a post which he held until the enforcement of the Test Acts in Tangier in 1666. Why has he not appeared subsequently in lists of Colonels? Several reasons. First, given the role of Kirke and the Regiment in the Dutch invasion, it was politically undesirable to admit to an Irish catholic having commanded the Regiment in Tangier, at a time when legally, despite the practice of the King in preferring Catholics, the Test Acts forbade this. Secondly, Davis’s history is vague in many areas concerning the early years of the Regiment, and has established the incorrect view that the Queen’s sprang from only one root origin in 1661.