The commander of the Confederate army was General Robert E. Lee. Lee was originally offered command of the Union Army by President Lincoln, but he rejected the offer because he didn't want to fight against his fellow Virginians.
General Robert E. Lee was a lifetime military officer. He attended the United States Military Academy at West Point and graduated second in his class. After refusing President Lincoln's offer to lead the Union Army, Lee joined the newly formed Confederate Army when Virginia seceded from the United States. He attempted to invade the North several times but was ultimately unsuccessful. In 1865, Lee surrendered to General Ulysses S. Grant at the Appomattox Courthouse to end the Civil War.