Changes

After the 1860 Election of Abraham Lincoln, Mallory urged conciliation (as did many other eventual prominent Southern politicians, including Jefferson Davis). However, like many others, his loyalties lay with the South, and when Florida seceded, he followed. Because of his friendship with President Davis, the need of a Floridian cabinet member, and his extremely useful and vast knowledge of naval affairs, he was appointed Secretary of the Navy.

At the start of the war, though, the Confederacy barely owned fifteen warships and very few naval officers had seceded. Also, the Confederate War Department did not cooperate very efficiently, and naval funding was very limited. However, Mallory was somewhat effective in finding some European ships, mainly from Great Britain. Arguably his most important British acquisition was the C.S.S. ''Alabama'', which was captained by Raphael Semmes, and was arguably the most famous Confederate raider. These raiders would mainly be used to attack merchant shipping, possibly diverting some blockade ships and ruining the Union blockade (which was slowly choking the South). Also, his vision of creating many ironclad warships to destroy the mainly wooden warships of the Union blockades was not fulfilled, mainly because of the main Southern disadvantage: a lack of funds and materiel. In a related sense, his most important "failure" was not being able to persuade the other government officials to allot enough funding toward the navy.