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."
During the weeks before the Battle of Shiloh, the 18th Louisiana was one of the regiments called to the tiny crossroads town of Corinth, Mississippi, for Confederate General Albert Sidney Johnston's planned attack on Union forces encamped near Pittsburg Landing, Tennessee. At Shiloh, the 18th Louisiana was organized into Col. Preston Pond's brigade. It was while serving in this brigade that the regiment and their commander received their baptism by fire. Pond's brigade attacked the Federal right, against the divisions of Union generals William Tecumseh Sherman and John A. McClernand. During one of these attacks, Colonel Mouton was wounded. After this Confederate defeat in April 1862, General P.G.T. Beauregard ordered a withdrawal back to Corinth. After arriving there, the 18th Louisiana was sent back to Louisiana to replenish its depleted ranks.
While back in Louisiana, Mouton was made interim commander of the District of West Louisiana, part of the Trans-Mississippi Department, and did what he could with the limited men and supplies that he had to fight off Federal attempts to move into the state. His army, attempting to protect the sugar cane farms along Bayou Lafourche, was brushed aside by the U.S. Volunteers under Brigadier General Godfrey Weitzel in the Battle of Georgia Landing at Labadieville, Louisiana, in October 1862, which led to Weitzel destroying much of the crops in that area. With the arrival of Confederate Major General Richard Taylor, Mouton was made a brigade commander and given the rank of brigadier general. The duo of Mouton and Taylor would prove to be one of the most efficient during the war and they, along with cavalry commander Thomas Green, would harass, confuse, frustrate, and delay Union attempts to secure the Bayou Teche region of southern Louisiana. Mouton's leadership in his Louisiana brigade helped the Confederates undermine Union attempts to access the rich Bayou Teche region. He was a key participant in the battles of Irish Bend, Fort Bisland, Franklin, and Bayou Borbeau, along with numerous other smaller skirmishes.
Mouton's brigade was used as the lead unit in the Confederate attack at the Battle of Mansfield. While leading his brigade in a charge against the Union position, Mouton was shot and killed. Historian John D. Winters reports on the battle: "On his horse, Mouton made a perfect target, and a Federal marksman dropped him from his saddle. The gallant Polignac now rode forward and took over the command. With tears of grief and rage in their eyes, the yelling men followed Polignac. They ran on through the deadly hail, determined to avenge the death of their leader. ... Mouton's division lost about one third of its total strength."[2] Mouton's death was lamented by General Taylor, who said, "Above all the death of the gallant Mouton affected me ... modest, unselfish, and patriotic. He showed best in action always leading his men." He was first buried on the battlefield but was moved in 1874 to St. John's Cemetery in Lafayette, Louisiana.
Mouton's stepmother was the sister of Confederate General Franklin Gardner.