Life changed decidedly for the worse for the indigenous peoples of Honduras after the arrival of the Spanish.  Honduras was overlooked by the Spaniards for some time, but once they began to conquer it things went downhill quickly.  First of all, communicable diseases ravaged the native population who had no immunity to the microscopic enemies carried by their oppressors.  Many natives were mistreated and abused by the Spaniards and a large number were sold into slavery in the Carribbean. 

The discovery of precious metals in Honduras brought more settlers and increased the demand for indigenous slave labor, which eventually led to a massive and successful revolt in 1537.  After successfully defending against all attacks, their leader (Lempira) was assassinated during negotiations and the rebellion crumbled.  The following year saw the native population cut in half at the hands of the Spanish, and the remaining few thousand were divided into encomiendas and placed under the rule of Spanish settlers.  Under the encomienda system the natives were further exploited as a labor source.