In 1509 King Ferdinand gave Christopher Columbus’s son, Diego, the title of Governor of the Indies with the duty to organize an exploratory expedition led by Diego Velázquez de Cuellar (1465–1524). In 1511 four ships from Spain arrived carrying 300 settlers under Diego Columbus and his wife, María de Toledo (grandniece of King Ferdinand). Also on board was tall, portly, blond Velázquez, the new governor of Cuba, and his secretary, young Hernán Cortés (1485–1547), who later set sail from Havana  for Mexico to subdue the Aztecs.
Velázquez founded the first town at Baracoa  in 1512, followed within the next few years by six other crude villas—Bayamo, Puerto Príncipe (today’s Camagüey), San Cristóbal de la Habana, Sancti Spíritus , Santiago de Cuba, and Trinidad —whose mud streets would eventually be paved with cobblestones shipped from Europe as ballast.
The Spaniards were not on a holy mission. The Spaniards had set out in quest of spices, gold, and rich civilizations. Thus the indigenous island cultures—considered by the Spaniards to be a backward, godless race—were subjected to the Spaniards’ ruthless and mostly fruitless quest for silver and gold.
A priest named Bartolomé de las Casas (1474–1566) accompanied Velázquez and recorded in his History of the Indies:
The Indians came to meete us, and to receive us with victuals, and delicate cheere… the Devill put himselfe into the Spaniards, to put them all to the edge of the sword in my presence, without any cause whatsoever, more than three thousand soules, which were set before us, men, women and children. I saw there so great cruelties, that never any man living either have or shall see the like.
Slavery was forbidden by papal edict, but the ingenious Spaniards immediately found a way around the prohibition. Spain parceled its new conquests among the conquistadores. The Indians were turned into peones—serfs under the guise of being taught Christianity. Each landowner was allotted from 40 to 200 Indian laborers under a system known as the encomienda, from the verb “to entrust.” Those Indians not marched off to work in mineral mines were rounded up and placed on plantations. Since the Indians were supposed to be freed once converted, they were literally worked to death to extract the maximum labor.
The Indian resistance was led by Hatuey, an Indian chieftain who had fought the Spanish on the island of Hispaniola and fled to Cuba after his people were defeated. Eventually the Spaniards captured the heroic Indian chief and burned him at the stake on February 2, 1512. Thus the Spaniards, in their inimically cruel fashion, provided Cuba with its first martyr to independence.
The 16th century witnessed the extinction of a race. Those Taíno not put to the sword or worked to death fell victim to exotic diseases. Measles, smallpox, and tuberculosis also cut down the Taínos like a scythe. They had no natural resistance to European diseases. Within 100 years of Columbus’s landfall, virtually the entire indigenous Cuban population had perished.
The Spanish found little silver and gold in Cuba. They had greater luck in Mexico and Peru, whose indigenous cultures flaunted vast quantities of precious metals and jewels. Cuba was set to become a vital stopover for Spanish galleons and traders carrying the wealth of the Americas back to Europe.
In 1564 a Spanish expedition reached the Philippines. The next year it discovered the northern Pacific trade winds that for the next 250 years propelled ships laden with Chinese treasure to Acapulco, from where the booty was carried overland to Veracruz, on the Gulf of Mexico, and loaded onto ships bound for Havana  and Europe. Oriental perfumes, pearls, silks, and ivories passed through Havana. To these shipments were added silver from Bolivia, alpaca from Peru, and rare woods from Central America, plus Cuban tobacco, leather, fruit, and its own precious woods. To supply the fleets, the forests were felled, making room for meats, hides, tobacco (and, later, sugar) for sale in Europe.
With the Indian population devastated, the Spanish turned to West Africa to supply its labor. By the turn of the century, an incredibly lucrative slave trade had developed. Landowners, slave traders, merchants, and smugglers were in their heyday—the Spanish Crown heavily taxed exports, which fostered smuggling on a remarkable scale. The Spaniards tried to regulate the slave trade, but it was so profitable that it resisted control.
As early as 1526, a royal decree declared that ships had to travel in convoy to Spain. En route, they gathered in Havana harbor. The crown had a vested interest in protecting the wealth from pirates; it received one-fifth of the treasure. In 1537, Havana  itself was raided. One year later, French pirate Jacques de Sores sacked the capital; when a bid by the Spaniards to retake the city faltered, de Sores razed it.
Soon, pirates were encouraged (and eventually licensed) by the governments of France, Holland, and England to prey upon Spanish shipping. In 1587 King Philip of Spain determined to end the growing sea power of England and amassed a great armada to invade her. Sir Francis Drake, John Hawkins, and Sir Walter Raleigh assembled a fleet and destroyed the armada, breaking the power of Spain in the Old World.
Now, no city was safe. There were hundreds of raids every year. Spain was impotent. In 1662, Henry Morgan, a stocky Welshman and leader of the Buccaneers, a motley yet disciplined group of pirates that would later operate under British license from Port Royal in Jamaica, ransacked Havana , pilfered the cathedral bells, and left with a taunt that the Spanish weren’t equal to the stone walls that Spain had built: “I could have defended Morro Castle with a dog and a gun.”
The Spanish Crown treated Cuba as a cash cow to milk dry as it pleased. For example, it had monopolized tobacco trading by 1717. The restriction so affected farmers’ incomes that the vegueros (tobacco growers) marched on Havana . The rebellion, the first against Spain, was brutally crushed. In 1740, Spain created the Real Compañía, with a monopoly on all trade between Cuba and Spain. It bought Cuban products cheaply and sold necessities from Europe at inflated prices.
On January 4, 1762, George III of England declared war on Spain. On June 7, a British fleet of 200 warships carrying 11,000 troops put ashore and Havana  erupted in panic. The Spanish scuttled three ships in the harbor mouth, ineptly trapping their own warships inside the harbor. That night, when Spanish guards atop the Cabaña began firing at British scouts, the Spanish warships began blasting the ridge, causing their own troops to flee. The British took the ridge and laid siege to Havana. On July 29 sappers blew an enormous hole in the Castillo de Morro, and the flag of St. George was raised over the city.
The English immediately lifted Spain’s trade restrictions. Foreign merchants flocked, and Cuba witnessed surging prosperity. Jamaican sugar planters, however, pressured England to cede back to Spain what would otherwise become a formidable rival for the English sugar market. On February 10, 1763, England exchanged Cuba for Florida in the Treaty of Paris. In the interim, Spain had acquired a more enlightened king, Charles III, who continued the free-trade policy. The boom continued, encouraged a decade later when the United States began trading directly with Cuba.