Leaving the Rifles, he entered the Confederate Army, and then the Confederate Navy, where he was commissioned acting master in December 1861, where he commanded a floating battery at Columbus, Kentucky. He was appointed lieutenant, March 18, 1862, serving at New Orleans on the . Following the Battle of Forts Jackson and St. Philip and prior to the surrender of Fort Jackson and Fort St. Philip, April 28, 1862, he was given permission by his immediate commander, John K. Mitchell, to abandon his vessel and to try and escape capture. He was then sent aboard the , at Memphis, Tennessee, and slightly wounded in action, July 15, 1862, during the ram's passage through the Federal fleet, above Vicksburg. He participated in the taking of the , at Newbern, North Carolina. He was then stationed aboard the , in 1863, as a lieutenant