In every major war, throughout the history of the United States, from the American Revolution through the Indian Wars, Native-Americans and African-Americans have fought with and against each other.
This scenario prevailed during the Civil War. Some tribes fought for the South, such as the Cherokees
while others assisted the North like the Seminoles.

Slaves and the black soldiers, who couldn't read or write, had no idea of the historical deprivations and the frequent genocidal intent of the U.S. government toward Native Americans. Free blacks, whether they could read and write, generally had no access to first hand or second-hand unbiased information on this relationship. Most whites who had access often didn't really care about the situation. It was business as usual in the name of "Manifest Destiny". Most Americans viewed the Indians as incorrigible and non-reformable savages. Those closest to the warring factions or who were threaten by it, naturally wanted government protection at any cost.

At the outbreak of the Civil War, the government was fighting the Indians in the west. It withdrew most of its men and resources from the Indian wars, to concentrate on ending the rebellion. At the end of the Civil War, 186,000 black soldiers had participated in the war, with 38,000 killed in action. Southerners and eastern populations did not want to see armed Negro soldiers near or in their communities. They were also afraid of the labor market being flooded with a new source of labor. General employment opportunities in these communities was not available to blacks, so many African-Americans took a long hard look at military service which offered shelter, education, steady pay, medical attention and a pension. Some decided it was much better than frequent civilian unemployment. Of course in some quarters, it was thought this is an good way of getting rid of two problems at the same time.

When Congress reorganized the peacetime regular army in the summer of 1866, it had taken the above situation into account. It also recognized the military merits of black soldiers by authorizing two segregated regiments of black cavalry, the Ninth United States Cavalry and the Tenth United States Cavalry and the 24th, 25th , 38th , 39th, 40th and 41st Infantry Regiments. Orders were given to transfer the troops to the western war arena, where they would join the army's fight with the Indians. In 1869, one year after the discharge of Cathay Williams, the female Buffalo Soldier in disguise, the black infantry regiments were consolidated into two units, the Twenty-fourth United States Infantry and the Twenty-fifth United States Infantry. All of the black regiments were commanded by white officers at that time.