[4] From January 1839 to November 1841, Hughes served aboard Commodore Alexander Claxton's flagship USS Constitution in the Pacific Squadron.

[3] From January to June 1843, Hughes served aboard the receiving ship USS Pennsylvania at the Norfolk Navy Yard.

From Fall 1849 to Summer 1850, Hughes was assigned to the receiving ship USS North Carolina at the New York Navy Yard.

Promoted to acting master, he served aboard the sloop-of-war USS Albany in the Gulf of Mexico and the West Indies for twenty-five months until Autumn 1852.

On 26 January 1856 under the leadership of Commander Guert Gansevoort, Hughes went ashore with seamen and marines at Seattle, Washington Territory to help repel an Indian attack on the settlers during the Puget Sound War.

[3] From Winter 1856 to Fall 1857, Hughes served as executive officer on the receiving ship USS Allegheny at the Baltimore Navy Yard.

He then served as a lieutenant and the executive officer on the stores ship USS Supply in the Brazil and Africa Squadrons until Autumn 1858.

Returning to the San Jacinto, he led the boarding party during the capture of the slave ship Storm King on 8 August 1860.

[7] From December 1860 to April 1861, Hughes was assigned to the receiving ship USS Princeton at the Philadelphia Navy Yard.

In May 1862, Hughes was reassigned as commanding officer of the gunboat USS Mohawk in the South Atlantic Squadron after having sailed the Water Witch north for repairs.

[3] In October 1864, Hughes was detached from the Cimarron to serve as ordnance officer for the Mississippi Squadron on the staff of acting Rear Adm. S. P. Lee until February 1865.

[3] In April 1866, Hughes was assigned as a member of the Naval General Court Martial at Philadelphia, serving until June 1866.

From 1877 to 1878, Hughes served as commandant of the Port Royal Naval Station on Parris Island in South Carolina.