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There is a lot of confusion about this. People today usually do not know that both the Union and Confederacy had several field armies out fighting battles all through the war. Each of these field armies had a general in command. Usually when your question is asked people are looking for Robert E. Lee. For most of the war Lee actually commanded only a field army - the best and most famous one the Rebels had, the Army of Northern Virginia. Finally, in the last two months of the war Lee was made General in Chief over ALL the southern armies, but by then it was too late.

For most of the war the actual highest ranking Confederate general was a man few have heard of today, Samuel Cooper. Cooper was actually from New Jersey, but had married a Virginia girl, and went south with her when the war came. He was called the General in Chief for most of the war, but really spent the entire war in Richmond as a glorified clerk. This was because the Confederate president, Jefferson Davis, considered himself to be as much a military expert as anyone on the south. He had graduated from West Point, become a hero in the Mexican War, and had first married a daughter of General (later president) Zachary Taylor. Davis liked to micromanage the army and left no room for his general in chief, or for his Secretary of War, to do much more than shuffle papers.

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