After service in a number of ships and stations ashore, he reached the high point in his career during the Spanish-American War. He was Executive Officer of Petrel during the Battle of Manila Bay. Immediately after the action, he commanded a small boat which boarded and set fire to five Spanish ships lying in Cavite Harbor, despite reports that fuzes had been set to their magazines and in the face of a large and excited armed force on shore nearby. He was advanced five numbers in rank for eminent and conspicuous conduct on this occasion.
Commander Hughes died at Yokohama, Japan, 28 September 1903.