Answer:
The Union Army went through eight Commanders during the Civil War. They were George McClellan (twice), John Pope, Ambrose Burnside, Irvin McDowell, Joseph Hooker, George Meade, and U.S. Grant.
The Confederates were not organized the same way. Robert E. Lee was not the Commander of all the Confederate troops. He was Commander of the Army of Northern Virginia, which fought in the eastern theater of the war. The overall Commander of the Army was the President Jefferson Davis.