Gatlin was appointed
adjutant general of North Carolina, with the rank of
major general of militia, and received the commission of colonel of infantry in the regular army of the
Confederate States of America. He was then given command of the Southern department, coastal defense, with headquarters at
Wilmington, North Carolina. He was promoted to
brigadier general in August 1861 and was assigned to command the department of North Carolina and the coastal defenses of the State. Soon after Gatlin was promoted to command, Fort Hatteras was captured by the Union. Gatlin then made preparations for the defense of
New Bern. He made his headquarters at
Goldsboro in September and there organized troops and prepared for the defense of the area. Upon his suggestion, an additional coastal district was formed and General
Daniel H. Hill was made commander of the new district. Gatlin repeatedly requested reinforcements, but none were available and in March 1862, New Bern fell. Gatlin was suffering from a severe illness and on March 19, 1862, he was relieved from duty. In his final report he stated that "we failed to make timely efforts to maintain the ascendancy on Pamlico sound, and thus admitted
Burnside's fleet without a contest; we failed to put a proper force on
Roanoke island, and thus lost the key to our interior coast, and we failed to furnish General
Branch with a reasonable force, and thus lost the important town of New Bern. What I claim is that these failures do not by right rest with me." Gatlin resigned in September 1862 but subsequently served as adjutant and
inspector general of North Carolina. ==Post-war==