Hughes was commissioned lieutenant on 7 November 1774, and by the end of 1780 had become the first lieutenant of the Seahorse 24, Captain John Panton, serving in the East Indies. Early in the following year he brought her into Bombay after Panton had died at Malacca and she had been reduced to a wreck, his apparent popularity with the exhausted men being a key factor in keeping them at the pumps.
He became flag-captain to Commodore Richard King aboard the Exeter 64 in February 1782 after Captain Henry Reynolds had lost his life at the Battle of Sadras, and was officially posted captain with seniority from 1 March. The Exeter suffered casualties of four men killed and forty wounded at the Battle of Providien on 12 April, and after transferring with King to the Hero 74 Hughes fought at the Battle of Negapatam on 6 July where he lost twelve men killed and twenty-three wounded and had to raise a signal of distress towards the end of the engagement. He then fought at the Battle of Trincomale on 3 September where his command lost one man killed and seventeen wounded. Following the death of Captain Charles Wood on 9 October from injuries received at the Battle of Trincomale Hughes replaced that officer aboard the Worcester 64, and he commanded her at the Battle of Cuddalore on 20 June 1783 where she lost eight men killed and thirty-two wounded.
When the Worcester was ordered home Hughes transferred into the Bristol 50 in April 1785, and in the same year he hoisted his broad pennant as the commodore and commander-in-chief of the much reduced East Indies station. He subsequently brought the Bristol home in July 1786, and she was paid off later that year.
Hughes did not see any further service, and it being deemed that his service did not warrant promotion to flag rank he became a superannuated captain on 23 April 1804. He died some time after 1811.
Hughes was married, but his wife pre-deceased him on 11 April 1797. His residence was at Friday Hill House, Chingford, Essex.
He was held in very high regard by his men.