Confederate Armies & Departments in the Eastern Theater

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On April 12 the Army of Northern Virginia, formerly the Confederate Army of the Potomac under the command of General Joseph Johnston, merged with the  Army of the Peninsula, Department of Norfolk and the Aquia District. General Johnston and others would continue to refer to the army using its older name until Robert E. Lee took command on June 1, when the name change became permanent.

The Army of the Valley under Major General Thomas Jackson retreated up the Shenandoah Valley while he prepared his next move.
The Army of the Peninsula  under the command of Major General John Magruder merged into the Army of Northern Virginia as its Right Wing.
On April 27 the Department of Norfolk under the command of Major General Benjamin Huger was ordered by General Johnston to abandon the Norfolk area, salvaging what he could from the Gosport Navy Yard. 
The Aquia District, commanded by Major General Gustavus Smith, merged into the Army of Northern Virginia as part of the Center Division.