Col. John S. Marmaduke, CSA
The Union deployed a mix of Regulars and Missouri troops; the Confederates had some Missouri State Guards.
The US forces lost 31 men, the Confederates about 50.
Claiborne Jackson, the pro-Southern Governor of Missouri, wanted the state to secede and join the Confederacy. Union Brig. Gen. Nathaniel Lyon wanted to suppress Jackson's Missouri State Guard, commanded by (ex-Governor) Sterling Price. Reaching Jefferson City, the state capital, Lyon discovered that Jackson and Price had pulled his ill-armed men back towards Boonville rather than fight at a disadvantage.
Lyon wasn't going to let his prey get away. He reembarked on steamboats, transported his men to below Boonville, marched to the town, and attacked. In a short fight, Lyon dispersed the Confederates, commanded on the field by Col. John S. Marmaduke, and occupied Boonville. This early victory established Union control of the Missouri River and helped douse attempts to place Missouri in the Confederacy. It was especially important since most of the Southern sympathizers in Missouri were in the Missouri River Valley ' precisely where Lyon won the battle.