The three Indian Home Guard regiments were mustered in Kansas and were regular US troops though they were not US citizens and most of them were citizens of nations allied with the Confederacy. They saw service in Missouri and Arkansas, though of course the Indian Territory (present Oklahoma) was the home of the vast majority of the Indian soldiers (A small number of the Indian soldiers were from Kansas). They enrolled with the 'understanding' they were to reclaim their home countries and the US had the intention of using them to return/protect the refugees from camps in Kansas and Missouri to the Indian Territory which was their primary role but they were engaged at Prairie Grove and scouted from Ft Gibson into western Arkansas and were supplied from Rhea's Mills and Dutch Mills.

The Indian nations allied with the Confederacy could not be ordered outside their boundaries without their consent, which they gave on a few occassions (Pea Ridge, Newtonia, Ft Smith, Jenkin's Ferry). It appears that detachments from Watie's Cherokee regiments operated with Livingston and perhaps Quantrill at times.