After the peace he commanded the squadron in the 'Streights' (of Gibraltar) – what would later become the Mediterranean fleet – against the Barbary pirates and then became Comptroller of the Navy. The painting is inscribed 'Sir Thomas Allin' and is one of the 'flagmen' series commissioned by Charles II's brother James, Duke of York, after the Battle of Lowestoft. This was the first major action of the Second Dutch War, in which James commanded the fleet. It is one of those which Pepys noted as begun or finished when, with Allin and Admiral Sir William Batten, he visited Lely's studio on 18 April 1666.

Lely, a Dutchman who arrived in England in 1641 after the death of van Dyck, soon became his successor as leading portraitist of the day. He worked for Charles I, continued to flourish under the Commonwealth and Protectorate, and after the Restoration of 1660 was appointed Principal Painter to Charles II. The full 'flagmen' set consists of 13 individual portraits, of which George IV presented 11 plus a copy of that of Admiral Sir John Lawson (BHC2833) to Greenwich Hospital in 1824. The originals of Lawson and of Prince Rupert were retained in the Royal Collection, although William IV presented an extended full-length copy of the latter (BHC2990) to the Hospital in 1835.