He commanded the screw frigate in the North Atlantic Blockading Squadron in 1864–65, and a division of Admiral Porter's Squadron at the two battles of Fort Fisher in December 1864 and January 1865. Thatcher was then appointed to command of the Western Gulf Squadron, immediately commencing operations in cooperation with General Canby, commander of the Army of West Mississippi, in the capture of Mobile, Alabama. After a brief and vigorous bombardment, Spanish Fort and Fort Blakeley were captured by the Union Army on 9 April 1865. With the key defences of the city lost, the Confederate troops evacuated Mobile on April 12. A formal surrender was demanded by General Granger and Acting-Rear Admiral Thatcher, and possession taken of the city.