When leaving the Island for Spain, Christopher Columbus left a few of his men behind at La Navidad; about 36 to keep an eye on things, only to find them all slaughtered upon his return with 13.000 more men the following year; and La Navidad, burned to the ground.
The Taino were famously peaceful; so what could have possibly caused them to kill the Spaniards? Well, after the departure of Christopher Columbus, the Tainos quickly realized that these men were not "gods". Christopher Columbus found a journal of one of his soldiers; Guillermo Coma, with a passage explaining what had happened. 

"Bad feelings had arisen and had broken out in warfare, because of the licentious conduct of our men towards the Indian women, for each Spaniard had five women to minister his pleasure."

The Spaniards raped their women and reduced most of the men to slavery; greedy to find more gold. Caonabo who was the husband of the Queen of Xaragua, Anacaona; plotted against them and killed them all. He would later be captured, imprisoned,
then shipped to Spain; the ship transporting him, would sink before making it to Europe.