Upon returning to the United States, Guthrie found out that his home state had joined the Confederacy and now he had to chose which side to serve. Despite a plea from a good friend, Captain Andrew H. Foote, he resigned his Federal commission and was appointed a CSN lieutenant on July 13, 1861.
Posted to New Orleans, on November 7, he was given command of the steamer CSS Red Rover (which was captured and turned into the Union hospital ship USS Red Rover). On December 11, he also assumed command of the floating battery New Orleans, formerly the Pelican drydock.
Early in March 1862, he took both vessels up to Island No. 10, but once there was detached from them and sent to Memphis to assist in the outfitting of the new Confederate ironclad ram CSS Arkansas. To prevent her capture, the Arkansas was moved up the Yazoo River to Greenwood, Mississippi, but then very little more work was done on her until early May when the dynamic Lt. Isaac Newton Brown was ordered to make her ready for battle.
John Guthrie and the ship's commander, William McBlair were transferred elsewhere.