I have a theory (I have many theories if you've ever noticed). The history books tell us that the Taino, the people indigenous to this island were completely wiped out by enslavement or disease within 40 years of European arrival. However I think that is highly unlikely for several reasons:

1. This is a big mountainous place, with extremely difficult terrain, and there are still areas even today which are hard to get to and where few 'europeans' have ever been, even 500 years later. So I doubt that in 40 years, Columbus and his associates could have reliably confirmed the complete extinction of an entire nation

2. During slave revolts in the French colony, the rebels were able to successfully hide in the mountains for decades, and ultimately were able to successfully drive the French from the island. Even in the early 1900's, the Caco warriors hiding out in the Central Plateau of Haiti were able to wage a not insubstantial resistance against US marines for a number of years.

3. Island dwellers have been demonstrated to have much more significant open water navigation skills that has often been thought (see Guns, Germs, and Steel). I suspect there was likely considerable inter island and Central America coastal travel by the Taino, Arawaks, Caribs and others long before 1492.

This all leads, to the possibility that the Taino may have quietly cleared out of the coastal areas where the colonial towns and plantations were popping up, and headed for the hills, or even more likely out to sea. If anyone has knowledge of this subject, I'd love to hear from you.