This was the title of General Johnston's army in Virginia before he was wounded and disabled. General Lee renamed this command Army of Northern Virginia.
http://en.wikipedia.org/wiki/Confederate_Army_of_the_Potomac

In the western theater of war the Confederate military command which attacked Grant at Shiloh and later marched into Kentucky was called the Army of the Mississippi. In November 1862 General Bragg renamed it the Army of Tennessee.
http://en.wikipedia.org/wiki/Army_of_Tennessee