In March of 1862, the Confederate Army of the Southwest under General Earl Van Dorn moved against Federal forces in northwest Arkansas in the first stage of an attempted invasion of Missouri. Confederate forces had been driven from the embattled state and Van Dorn hoped his campaign would secure Missouri for the Confederacy. On March 7,1862, Van Dorn led his 16,000-man army in an attack against 10,500 Union troops at their strongly fortified position on Pea Ridge. The fierce two-day engagement — the Battle of Elkhorn Tavern — was the largest battle of the War Between the States fought west of the Mississippi.

Three Confederate regiments at the Battle of Elkhorn Tavern were composed of American Indians from General Albert Pike's brigade. At the forefront of the fighting was the 1st Cherokee Mounted Rifles, commanded by Colonel Stand Watie. While the Cherokees were considered the most disciplined of Pike's Indian troops, many came to fight attired in traditional Cherokee battle dress.
"Their faces were painted, and their long straight hair, tied in a queue, hung down behind," recalled a Confederate observer. "Their dress was chiefly in the Indian costume — buckskin hunting shirts, dyed of almost every color, leggings, and moccasins of the same material.... They were straight, active, and sinewy in their persons and movements...."
At one point in the battle, as Federal artillery severely hammered Van Dorn's Confederates, Watie's troops advanced on foot in a bold charge. Facing scores of fierce-looking, shrieking Indian warriors, the Union artillery crews fled, leaving the 1st Cherokee Mounted Rifles in command of the battery.
After initial success on the battle's first day, Van Dorn's Confederates were hampered by the death of key commanders. Van Dorn retreated, leaving Missouri in Northern control, but among the last to leave the battlefield were Stand Watie's Cherokees.

The 1st Cherokee Mounted Rifles was organized in 1861 by Cherokee leader Stand Watie, who was appointed the regiment's colonel by the Confederate government. The only American Indian to become a brigadier general in Confederate service, Watie was a well-educated, successful farmer in the Indian Territory (modern-day Oklahoma) when the War Between the States began. Watie was among the Cherokee leaders who reluctantly signed the 1835 treaty that stripped the Cherokee of their Appalachian homeland and moved them to Oklahoma via the "Trail of Tears." He deeply resented his people's treatment by the Federal government and hoped that Southern independence would allow a better life for the Cherokee. In 1861, the Confederate government and Cherokee leaders ratified the Treaty of Cooperation established between the Confederacy and the Cherokee Nation. During the war, the Confederacy granted the Five Civilized Tribes of the Indian Nation rights long denied them by the Federal government.

The 1st Cherokee Mounted Rifles originally mustered about 300 troops. In an early campaign, the regiment attacked the Creek Indians who supported the Union and drove them from the Indian Territory into Kansas. Their most notable engagement was the Battle of Elkhorn Tavern. Later, Watie's brilliantly successful guerrilla raids made him famous as the "Red Fox." Watie and his bold horse soldiers often struck Union forces where least expected, such as the surprise raid which dispersed Federal troops at Neosho in May of 1862. The surprise tactics of Watie's Cherokees unnerved Federal troops on the frontier, who sometimes imagined they could hear Watie's laughter in a thunderstorm.
In August of 1862, Watie was elected Principal Chief of the Cherokee Nation and on May 6, 1864, he was commissioned a brigadier general in the Confederate army. One of Watie's principal wartime achievements was the capture of the Federal army steamer J.R. Williams, which Watie and his Cherokee troops surprised on the Arkansas River in June of 1864. They pounded the ship and its army troop escort with artillery and small arms fire until the Federals beached the ship and retreated. The Cherokees boarded the stricken vessel and retrieved a cargo estimated at $120,000, distributing desperately needed supplies and boosting Southern morale in the war's Trans-Mississippi Theater.
One of Watie's most successful guerrilla operations occurred in September of 1864, when he led his troops on a raid against Federal forces near Cabin Creek in the Indian Territory. Watie reported the capture of more than 200 enemy wagons containing an estimated $1.5 million in supplies. News of Lee's surrender in April of 1865 preempted Watie's plans to marshal thousands of Indian Confederates in a major strike against Federal forces in Kansas. On June 23,1865, General Watie and his Indian command became the last Confederate force to lay down its arms.