On the outbreak of the Civil War, he commanded the 18th Louisiana Infantry Regiment, where he proved a strict disciplinarian who was also notably friendly and sociable with the rank and file. Wounded at Shiloh, he was made a brigade commander under General Richard Taylor, with whom he successfully obstructed Union efforts to secure the Bayou Teche region of southern Louisiana. In the Red River Campaign, Mouton was killed at the Battle of Mansfield, while leading his men in a cavalry charge.