The Crow Creek massacre occurred around 1325 AD (that is, long before Columbus) in South Dakota, along the Missouri River. The victims were from a group of agriculturalists known as the 'Initial Coalescent people' who are thought to have migrated from the plains due to drought. There is evidence that the victims were malnourished and that several individuals had previous war wounds (healed scalpings, arrows embedded in bone, etc.). Additionally, they clearly felt threatened: a defensive ditch was under construction when the massacre occurred. The total number of victims is estimated at 486 people, which included men, women and children:

Disturbingly, many of the victims were tortured (including "tongue removal, decapitation, and dismemberment"), at least 90% of the people were scalped and their village was burnt. The victims were left to rot where they fell, and were apparently only buried some months later.
This event is quite possibly due to ecological stress but nonetheless serves as a clear existence proof of genocide and abject cruelty among prehistoric societies. Native Americans had clearly tasted evil before Europeans arrived; which is obvious, of course, except that recent intellectual history and popular opinion has denied such a thing was possible. This evidence, though, is incontrovertible.
