What advantages did the spanish have over the indigenous people of the americas?

First of all, the Spanish (along with the rest of the large European countries at the time) had guns and other military technology. With the advantage of having gunpowder, the Spanish were able to relatively easily conquer the indigenous peoples in the Americas.  Another point is the Spanish military training; the American civilizations had no military training that matched the strict codes of the European countries, so the precision of the Spanish helped them conquer.