The Cherokee in the American Civil War were active in the Trans-Mississippi and Western Theaters. In the east, Confederate Cherokees led by William Holland Thomas hindered Union forces trying to use the Appalachian mountain passes of western North Carolina and eastern Tennessee. Out west, Confederate Cherokee Stand Watie led primarily Native Confederate forces in the Indian Territory, in what is now the state of Oklahoma. The Cherokee partnered with the Confederacy in order to get funds, as well as ultimately full recognition as a sovereign, independent state.
Before Indian removal, the Cherokee Nation was centered in and around the Blue Ridge Mountains—southwestern North Carolina, southeastern Tennessee, western South Carolina and northeastern Georgia. The Cherokee attempted to address their grievances by taking their problems to the American Federal judicial system. In 1830, a delegation led by Chief John Ross defended Cherokee rights before the U.S. Supreme Court in Cherokee Nation v. Georgia. The Indian cases set a precedent in Indian Country but the United States still enforced removal of most of the Cherokee Nation to west of the Mississippi River, along what became known as the Trail of Tears. After the removals, the Cherokee Nation was based west of the Mississippi River. Some Cherokee remained in the Blue Ridge Mountains.
The Cherokee blamed the federal government and former United States President Andrew Jackson for the Trail of Tears. They had adopted "Southern ways" before their removal from the Southeast. Cherokee society held slavery as a primary institution throughout the pre-war period, instituting laws that explicitly prohibited primarily "black (or negro) slaves" from obtaining citizenship in their nation, and later "persons of color" altogether. Cherokee judiciary and legislative bodies promulgated similar laws regarding race and enslaved status as the Cherokee attempted to legally define themselves as equal to whites or European Americans, at the expense and exclusion of non-white and non-Indian groups, and in particular Blacks. The Cherokee aligned with the Confederacy in part due to their existing cultural, trading, and legal affinities with those states that had seceded. In addition, the Cherokee in Indian Territory opposed William Seward's campaigning in 1860 on behalf of Abraham Lincoln, when he said that Lincoln would open the Indian Territory for white settlement.
Chief of the Cherokee John Ross was adamant that the Union was not dissolved. However, another leader of the Cherokee, Stand Watie, joined the Confederate cause, and on June 1, 1861, began recruiting for all-Indian units that became part of the Confederate army. Full-blooded Cherokee tended to support Ross (who was primarily Scottish) while the mixed-blooded Cherokee supported the 3/4 Cherokee Stand Watie. Stand Watie in 1862 was elected Chief of the newly declared Southern Cherokee Nation.
For the duration of the war, a series of small battles and constant guerrilla warfare were waged by Cherokee in the Indian Territory. Stand Watie officially became the last Confederate general to end fighting on June 25, 1865, at Fort Towson, in the southeast portion of the Indian Territory. The terms of the armistice allowed Watie and his command, the First Indian Brigade of the Army of the Trans-Mississippi, to demobilize rather than surrender and go home with their arms.
During the Civil War, the Cherokee Nation had approximately 21,000 members with 3,000 of them serving in the Confederacy as soldiers.
Thomas' Legion, led by William H. Thomas, a European-American who was adopted Cherokee, were originally stationed outside Knoxville, Tennessee at Strawberry Plains, Tennessee. Their primary duty was to protect the Alum Cave, and harass Union troops that invaded Tennessee. While briefly working around Chattanooga, Tennessee in June 1862, Thomas personally captured a Union Soldier, after which each of his men vowed to capture at least one "Yankee" before the war was over.
The Legion would become infamous due to their actions on September 15, 1862. While trying to stop a Union advance through Baptist Gap, a popular leader among the Cherokee, Astoogahtogeh, was killed leading a charge. Enraged, the remaining Cherokee were driven to avenge him. In retaliation for Astoogahtogeh's death, the Cherokee scalped the dead Union soldiers after the battle. After the event was reported in newspapers, Union soldiers would fear the Cherokee, but Thomas feared for the reputation of the Cherokee, as he did not want his people to be seen as barbaric. The scalps were sent to be buried with the soldiers they originally came from.
After a number of Thomas' men were captured in February 1864, some were convinced by the Union that they were fighting for slavery, and thereafter fought for the Union. Others convinced their captors they also would defect to the Union side, but instead returned to Thomas and told him Union officials offered $5,000 for Thomas' scalp. After this, many of his men were sent to fight in Virginia, some of whom were present at Appomattox Court House for General Robert E. Lee's surrender. The rest of the Legion continued to fight until surrendering along with the commanding officer of the District of Western North Carolina to the Union commander they had captured on 10 May 1865.
In May 1861, William H. Thomas began recruiting Cherokees from the Quallatown, North Carolina area. The first two companies were composed mostly of Indian soldiers. They were called the Junaluska Zouaves. Thomas' Confederates were sometimes referred to as Thomas' Legion or Thomas' Legion of Cherokee Indians and Highlanders. They were later designated as the 69th North Carolina Regiment.
The eastern Cherokee faced a severe smallpox outbreak following the war. Thomas and many of his followers were deeply in debt, to the point that the federal government recognized the eastern tribe as separate from the western tribe, and filed a lawsuit against the Cherokee's creditors, in effect leaving the protection of the Cherokee to the federal government.
In the west, at the end of the war, with the Union victorious, the Union Cherokee established policies that confiscated land from the Confederate Cherokee. The Federal government promised the Confederate Cherokee that the laws promoting the confiscation would be annulled. This was due to Indian Commissioner D.N. Cooley, who saw opportunities in splitting the factions of the Cherokee, as represented by Ross and Watie. Cooley even went as far as to portray Ross as a traitor, when Ross had always been a Union advocate. The Cherokee were forced to adopt their slaves into the tribe, and to allow settlement of their lands by whites. In effect, due to the Cherokee split and the maneuverings of Cooley, the Cherokee suffered the worst of Reconstruction.
Monuments were dedicated for the Cherokee's wartime participation in the early 20th century.
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