The United States Army in the Eastern Theater

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After March 11, 1862 there was no commander in chief of the army. McClellan had been relieved so that he could concentrate on commanding the Army of the Potomac in the Peninsula Campaign, while President Lincoln and Secretary of War Stanton commanded the Federal forces.

Army of the Potomac
Major General George B. McClellan

Department of Virginia
Major General John E. Wool

Middle Department
Major General John Dix

Mountain Department
Major General John C. Fremont

Department of the Rappahannock 
Major General Irvin McDowell