"freebooter, guerrilla," American English, 1858, originally "irregular or marauder during the 'Bleeding Kansas' troubles" (especially one who came from the North). It seems to have come into widespread use only during the Civil War. There was said to have been a bird of this name, but evidence for it is wanting. Perhaps a disparaging use from jay (n.). Hence back-formed verb jayhawk "harass" (1866).
Bushwhackers are men, united together, but not soldiers, who live in the bush; and whose avowed object is to kill every Union soldier they can, and cripple, so far as they can, the resources of the Federal military power. The jayhawkers are thieves. They plunder indiscriminately from all parties. In the same band are both rebel and Union men. ... Guerilla bands are companies enlisted and sworn into the rebel service; but not belonging to the armies. [Henry M. Painter, "Brief Narrative of Incidents in the War in Missouri," Boston, 1863.]