During the first half of the 16th century, the Cuban natives were basically wiped out. They would be replaced by Spanish settlers in the coming years.
Many were murdered by Spanish troops, while others were enslaved in mines to search for gold. The conditions there were bad enough to kill most of them; indeed, by the mid 1500s, most of the native population had died.
Some Indians, led by Hatuey, fought against the Spanish. Their rebellions were ruthlessly put down, and Hatuey was captured and burned alive.
As a result, the Spanish began importing slaves. This started as early as 1512, and continued until 1865. Tens of thousands of slaves were brought from Africa and other places to replace the dead natives.
Though little gold was found in Cuba, much was found in the rest of Latin America. Cuba served as a stop-over point to these areas.
In 1607, Havana became Cuba's capital. A government was formed, and municipalities were established. The island became quite prosperous from its position as a Spanish hub and its sugar production.
However, the island was plagued by piracy. Pirates would capture ships headed to Cuba or raid cities. No city was safe, and this caused many problems.