Since the first landing of Christopher Columbus in 1492, Native Americans were grossly mistreated, with many of them being enslaved, forced to convert to Christianity or murdered. Queen Isabella of Spain had actually decreed that the Natives were to be treated as subjects of the Spanish empire, and would therefore have the same rights as citizens, although this was almost immediately ignored.
In fact, Christopher Columbus, against the orders of Queen Isabella, enslaved 500 Natives and sent them to Spain. When Queen Isabella heard of this, she said the slaves were to be freed and sent back to Hispaniola. This would be the beginning of a long-standing conflict between the policy of Spain and the actual actions that were carried out during the colonial period.
The Natives were constantly brutalized. When some rebelled, they were either killed or captured as prisoners of war and then enslaved. Each Native was required to bring the Spanish a certain amount of gold every 90 days. Failing to do so resulted in execution.
This brutal treatment of Native Americans extended to other territories, like Puerto Rico, Cuba and Jamaica. The Natives virtually disappeared from these areas, as most were either murdered or killed by the bacteria of European diseases, of which they had no biological immunity.
New laws, called "encomienda," were created that declared the Natives were part of the land. So, when settlers bought land, they also bought the inhabitants of the area. The Natives were then legally forced into enslavement. A similar law, called "mitad," forced Natives who lived within 30 miles of a mine to work there for 6 months. The work was deadly and almost always fatal, where only 1/5 of those sent to work in the mines survived.