The Taino Indians, who came from South America, inhabited the major portion of the island when the Spaniards arrived. The Taino Indians, lived in small villages, organized in clans and led by a Cacique, or chief. They were a peaceful people who, with a limited knowledge of agriculture, lived on such domesticated tropical crops as pineapples, cassava, and sweet potatoes supplemented by seafood.

On November 19 1493, Christopher Columbus sailed to the island in his second voyage to the New World. He found the island populated by as many as 50,000 Taíno Indians. The Taino Indians who greeted Columbus made a big mistake when they showed him gold nuggets in the river and told him to take all he wanted. Originally the newcomers called the island San Juan Bautista, for St. John the Baptist and the town Puerto Rico because of its obvious excellent potentialities. It was not until later that the two names were switched. Thanks in part to the enthusiasm of ambitious Juan Ponce de León, a lieutenant to Columbus, the city of Puerto Rico ('rich port') quickly became Spain's most important military outpost in the Caribbean.

In 1511, The Taino Indians' after learning that the Spanish were mortal, revolted against Spaniards with no success. African Slaves were introduced into the island two year later to work on plantations as slaves. In 1539, concerned about potential threats from European enemies and recognizing the strategic importance of Puerto Rico, Spain began constructing massive defenses around San Juan. The construction of San Felipe del Morro Castle began. The fort featured 18-foot-thick walls; San Cristóbal and San Geronimo Forts also garrisoned troops, were built with the financial subsidy from the Mexican mines. Next the Spaniards constructed a wall, parts of which still survive, around the entire city. In 1625, Holland attacks San Juan, under the leadership of Boudewijn Hendrick (Balduino Enrico), besieging El Morro and La Fortaleza, burning the city, but the Spanish repel the Dutch troops

In 1873, The Spanish Crown abolished slavery in Puerto Rico. Leaders of the Puerto Rican abolitionist movement, including José Julián Acosta, Francisco Mariano Quiñones, Julio L. de Vizcarrondo, Ramón Emeterio Betances and Segundo Ruiz Belvis, waged a long struggle to end slavery on the island.