Watie led the Southern Cherokee delegation to Washington, D.C., after the American Civil War to sue for peace, hoping to have tribal divisions recognized.

Along with his two brothers and sisters, Watie learned to read and write English at the Moravian mission school in Spring Place, Cherokee Nation (now Georgia).

[2] Stand Watie occasionally helped write articles for the Cherokee Phoenix newspaper, for which his older brother Elias served as editor from 1828 to 1832.

In 1832, Georgia confiscated most of the Cherokee land, despite federal laws to protect Native Americans from state actions.

The state sent militia to destroy the offices and press of the Cherokee Phoenix, which had published articles against Indian Removal.

[5] Believing that removal was inevitable, the Watie brothers favored securing Cherokee rights by treaty before relocating to Indian Territory.

[9] In 1861, Principal Chief John Ross signed an alliance with the Confederate States to avoid disunity in Indian Territory.

In the summer of 1862, Ross removed the tribal records to Union-held Kansas and then proceeded to Washington, D.C., to meet with President Lincoln.

[12] Following Lincoln's Emancipation Proclamation in January 1863, Pegg called a special session of the Cherokee National Council.

After many Cherokee fled north to Kansas or south to Texas for safety, pro-Confederates took advantage of the instability and elected Stand Watie principal chief.

Open warfare broke out between Confederate and Union Cherokee within Indian Territory, the damage heightened by brigands with no allegiance at all.

[15] In August 1862, after John Ross and his followers announced their support for the Union and went to Fort Leavenworth, the remaining Southern Confederate minority faction elected Stand Watie as principal chief.

[17] Watie commanded the First Indian Brigade of the Army of the Trans-Mississippi, composed of two regiments of Mounted Rifles and three battalions of Cherokee, Seminole and Osage infantry.

They fought in a number of battles and skirmishes in the western Confederate states, including the Indian Territory, Arkansas, Missouri, Kansas, and Texas.

Watie took part in what is considered to be the greatest (and most famous) Confederate victory in Indian Territory, the Second Battle of Cabin Creek, which took place in what is now Mayes County, Oklahoma on September 19, 1864.

Union reports said that Watie's Indian cavalry "killed all the Negroes they could find", including wounded men.

[2] On June 23, 1865, at Doaksville in the Choctaw Nation (now Oklahoma), Watie signed a cease-fire agreement with Union representatives for his command, the First Indian Brigade of the Army of the Trans-Mississippi.

[14][21][22] In September 1865, after his demobilization, Watie went to Texas to see his wife Sallie and to mourn the death of their son, Comisky, who had died at age 15.

The Northern Cherokee suggested adopting them into the tribe, but wanted the federal government to give the Freedman an exclusive piece of associated territory.

[25] The tribe was strongly divided over the treaty issues and a new chief was elected, Lewis Downing, a full-blood and compromise candidate.

[27] One source states that Stand Watie married four women: Eleanor Looney, Elizabeth Fields, Isabella Hicks, and Sarah Caroline Bell.