The Marine Corps were to play a moderate role in the American Civil War (1861–1865) and were basically overshadowed by the confrontations of the land forces. Their most prominent task was blockade duty, and the strategic significance of the Federal blockade of southern ports, and the struggle for the Mississippi River were of real importance.  A battalion of Marines was to take part in the First Battle of Bull Run (First Manassas).

As more and more states seceded from the Union, about half of the Corps' officers left the Union to join the Confederacy and form the Confederate States Marine Corps, which ultimately played little part in the war