Upon his promotion to commander on July 16, 1862, Ammen assumed command of the gunboat USS "Sebago", which he commanded only for a brief period. He was ordered to Washington, D.C., in October 1862 and joined the monitor USS "Patapsco", which was just launched. The "Patapsco" was commissioned in January 1863, and Ammen joined with her the South Atlantic Blockading Squadron.