Seniority in the regular confederate service was decided by what year you graduated from West Point. In the case of Lee and Johnston, Lee was his superior because he had a better standing in their class. By the end of the war Lee was actually the highest ranking Confederate General. In 1865 he was made Commander in Chief of the remaining southern forces.
Order of Seniority:
Samuel Cooper
A.S. Johnson
Robert E. Lee
Joe Johnston
Beauregard
Bragg(Provisional
CSA)
Kirby Smith(Provisional
CSA)
Longstreet (Senior Lt. General)
Who was the senior Major General in
CSA?
-Robert Dedrick