At the outbreak of the Civil War, Mouton organized a company of men from the local population in Lafayette Parish. The company consisted of mostly farmers from around the area. Mouton was elected captain of the company upon its organization. When the company was organized into the 18th Louisiana Infantry Regiment, he was elected colonel. Mouton quickly made a reputation for himself as a strict disciplinarian and an efficient drillmaster. However, after drill he mingled freely with his soldiers in camp, stopping to talk to anyone of the regiment. One of his soldiers had this to say about him: "As a drillmaster, he had few, if any, equals. I have seen him drill the regiment for an hour in a square, the sides of which ware equal to the length of his line of battle, without once throwing a company outside or recalling a command when given. He was a strict disciplinarian and allowed no deviation from orders either by officers or soldiers."