Military leadership in the American Civil War Military leadership in the American Civil War was influenced by professional military education and the hard - earned pragmatism of command experience . While not all leaders had formal military training , the United States Military Academy at West Point and the United States Naval Academy at Annapolis created dedicated cadres of professional officer s whose understanding of military science had profound effect on the conduct of the American Civil War and whose lasting legacy helped forge the traditions of the modern U . S . officer corps of all service branches . The Union . Civilian Military Leaders . President Abraham Lincoln was Commander - in - Chief of the Union armed forces throughout the conflict ; after his April 14 , 1865 assassination , Vice President Andrew Johnson became the nation ' s chief executive . Lincoln ' s first Secretary of War was Simon Cameron ; Edwin M . Stanton was confirmed to replace Cameron in January 1862 . Thomas A . Scott was Assistant Secretary of War . Gideon Welles was Secretary of the Navy , aided by Assistant Secretary of the Navy Gustavus Fox . Regular Army Officers . When the war began , the American standing army or " Regular army " consisted of only 1080 commissioned officers and 15 , 000 enlisted men . Although 142 regular officers became Union generals during the war , most remained " frozen " in their regular units . That stated , most of the major Union wartime commanders had significant previous regular army experience . Militia and political leaders appointed to Union military leadership . Under the United States Constitution , each state recruited , trained , equipped , and maintained local militia ; regiment al officers were appointed and promoted by state governors . After states answered Lincoln ' s April 15 , 1861 , ninety - day call for 75 , 000 volunteer soldiers , most Union states ' regiments and batteries became known as " Volunteers " to distinguish between state and regular army units . Union brigade - level officers ( general s ) could receive two different types of Federal commissions : U . S . Army or U . S . Volunteers ( ex : Major General , U . S . A . as opposed to Major General , U . S . V . ) . While most Civil War generals held volunteer or brevet rank , many generals held both types of commission ; regular rank was considered superior . Native American and international officers in Union Army . Reflecting the multi - national makeup of the soldiers engaged , some Union military leaders derived from nations other than the United States . Union Naval Leaders . The rapid rise of the United States Navy during the Civil War contributed enormously to the North ' s ability to effectively blockade ports and Confederate shipping from quite early in the conflict . Handicapped by an aging 90 ship fleet , and despite significant manpower losses to the Confederate Navy after secession , a massive ship construction campaign embracing technological innovations from civil engineer James Buchanan Eads and naval engineer s like Benjamin F . Isherwood and John Ericsson , along with four years ' daily experience with modern naval conflict put the U . S . Navy onto a path which has led to today ' s world naval dominance . The Confederacy . Civilian Military Leaders . Jefferson Davis was named provisional president on February 9 , 1861 , and assumed similar commander - in - chief responsibilities as would Lincoln ; on November 6 , 1861 Davis was elected President of the Confederate States of America under the Confederate Constitution . Several men served the Confederacy as Secretary of War , including Leroy Pope Walker , Judah P . Benjamin , George W . Randolph , James Seddon , and John C . Breckinridge . Stephen Mallory was Confederate Secretary of the Navy throughout the conflict . Former Regular Army Officers . In the wake of secession , many regular officers felt they could not betray loyalty to their home state , as a result some 313 of those officers resigned their commission and in many cases took up arms for the Confederate Army . Himself a graduate of West Point and a former regular officer , Confederate President Jefferson Davis highly prized these valuable recruits to the cause and saw that former regular officers were given positions of authority and responsibility . Militia and political leaders appointed to Confederate military leadership . The land of Davy Crockett and Andrew Jackson , the state militiary tradition was especially strong in southern states , some of which were until recently frontier areas . Several significant Confederate military leaders emerged from state unit commands . Native American and international officers in Confederate army . While no foreign power sent troops or commanders directly to assist the Confederate States , some leaders derived from countries other than the United States . Confederate Naval Leaders . The Confederate Navy possessed no extensive shipbuilding facilities ; instead it relied on refitting captured ships or purchased warships from Great Britain . The South had abundant navigable inland waterways , but after the Union built a vast fleet of gunboats , they soon dominated the Mississippi , Tennessee , Cumberland , Red and other rivers , rendering those waterways almost useless to the Confederacy . Confederates did seize several Union Navy vessels in harbor after secession , and converted a few into ironclad s , like the CSS Virginia . Blockade runners were built and operated by British naval interests , although by late in the war the C . S . Navy operated some . A few new vessels were built or purchased in Britain , notably the CSS Shenandoah and the CSS Alabama . These warships acted as raiders , wreaking havoc with commercial shipping . Aggrieved by these losses , in 1871 the U . S . government was awarded damages from Great Britain in the Alabama Claims .