The Confederate Army of the Potomac was short-lived. It merged with the Army of the Shenandoah during the First Battle of Bull Run, and eventually became the First Corps of the Army of Northern Virginia.
The army began as state troops mobilized along an "Alexandria line," a long front stretching across northern Virginia from the Blue Ridge Mountains to the Chesapeake bay. These troops were organized and Brigadier General Milledge Bonham was placed in command. He was soon replaced with General P. G. T. Beauregard, who was tasked with organizing and training the raw troops from throughout the South and planning a response to the Northern invasion around Alexandria.
In July 1861, Beauregard had some 20,000 troops massed around Manassas Junction behind a sluggish stream called Bull Run. They were organized into eight brigades with artillery and cavalry support. The brigades were commanded by Bonham, Richard Ewell, David Jones, James Longstreet, Philip St. George Cocke, Jubal Early, and Nathan Evans. Theophilus Holmes commanded the reserve brigade.
Union General Irvin McDowell was advancing with some 35,000 troops, the Army of Northeastern Virginia. Beauregard needed General Joseph E. Johnston's Army of the Shenandoah, some 12,000 men, to even up the odds with McDowell.
Johnston slipped away from the Shenandoah Valley and joined up with Beauregard. The two armies linked up on the Bull Run battlefield, with some of Johnston's army arriving as the battle was raging. Johnston outranked Beauregard, but mostly deferred to Beauregard's arrangements and plans for the upcoming battle. After the Confederate victory, the merger of the two armies was made permanent.
On October 22, 1861, the Department of Northern Virginia was created with Johnston commanding. It combined the District of the Potomac (Beauregard), the Valley District (Jackson), and the Aquia District (Holmes), and officially ended the Army of the Potomac. Beauregard's original army would comprise the First Corps of this new army, which would eventually become known as the Army of Northern Virginia. Johnson commanded until he was seriously wounded at the Battle of Seven Pines on May 31, 1862, and was replaced by General Robert E. Lee.