On April 27, 1862, the Mercedita, under Henry Stellwagen's command, captured the blockade-runner Bermuda.
On Jan. 31, 1863, Stellwagen was in command of the USS Merceidta when it was attacked by the Confederate ironclad CSS Palmetto State. He surrendered the ship, but then took it out of action to a Union base.
After that he commanded the old sailing frigate/sloop USS Constellation on duty in the Mediterranean Sea on May 31, 1864, it was detached from the Mediterranean Station and ordered to report to the West Gulf Blockading Squadron under Admiral Farragut.
During his duty there, he received a sword from Britain for his service on the USS Constellation for its actions saving the British brig Mersey.
From February 23-25, he commanded a squadron from Charleston in his USS Pawnee which was sent out to capture and occupy Georgetown, S.C..