The history of Puerto Rico began with the settlement of the Ortoiroid people before 430 BC. At the time of Christopher Columbus's arrival in the New World in 1493, the dominant indigenous culture was that of the Taíno. The Taíno people's numbers went dangerously low during the later half of the 16th century because of new infectious diseases, other exploitation by Spanish settlers, and warfare.

Located in the northeastern Caribbean, Puerto Rico formed a key part of the Spanish Empire from the early years of the exploration, conquest and colonization of the New World. The island was a major military post during many wars between Spain and other European powers for control of the region in the 16th, 17th, and 18th centuries. In 1593, Portuguese soldiers, sent from Lisbon by order of Phillip II, composed the first garrison of the San Felipe del Morro fortress in San Juan. Some brought their wives, while others married Puerto Rican women, and today there are many Puerto Rican families with Portuguese last names. The smallest of the Greater Antilles, Puerto Rico was a stepping-stone in the passage from Europe to Cuba, Mexico, Central America, and the northern territories of South America. Throughout most of the 19th century until the conclusion of the Spanish–American War, Puerto Rico and Cuba were the last two Spanish colonies in the New World; they served as Spain's final outposts in a strategy to regain control of the American continents. Realizing that it was in danger of losing its two remaining Caribbean territories, the Spanish Crown revived the Royal Decree of Graces of 1815. The decree was printed in Spanish, English and French in order to attract Europeans, with the hope that the independence movements would lose their popularity and strength with the arrival of new settlers. Free land was offered to those who wanted to populate the islands on the condition that they swear their loyalty to the Spanish Crown and allegiance to the Roman Catholic Church.

In 1898, during the Spanish–American War, Puerto Rico was invaded and subsequently became a possession of the United States. The first years of the 20th century were marked by the struggle to obtain greater democratic rights from the United States.

The Foraker Act of 1900 established a civil government, ending rule by American generals and the Department of War. A United States Supreme Court ruling Ortega v. Lara, , involving the Foraker Act and referring to the island as "the acquired country", soon affirmed that the Constitution of the United States applied within its territory and that any domestic Puerto Rican laws which did not conflict with the United States Constitution remained in force. The Jones Act of 1917, which made Puerto Ricans U.S. citizens, paved the way for the drafting of Puerto Rico's Constitution and its approval by Congress and Puerto Rican voters in 1952. However, the political status of Puerto Rico, an unincorporated U.S. territory, is an ongoing debate.

Pre-colonial (before 1508)

The settlement of Puerto Rico began with the establishment of the Ortoiroid culture from the Orinoco region in South America. Some scholars suggest that their settlement dates back 4000 years.Rouse, Irving. The Tainos : Rise and Decline of the People Who Greeted Columbus . An archeological dig at the island of Vieques in 1990 found the remains of what is believed to be an Ortoiroid man (named Puerto Ferro man) which was dated to around 2000 BC. The Ortoiroid were displaced by the Saladoid, a culture from the same region that arrived on the island between 430 and 250 BC.

Between the seventh and 11th centuries, the Arawak are thought to have settled the island. During this time the Taíno culture developed, and by approximately 1000 AD, it had become dominant. Taíno culture has been traced to the village of Saladero at the basin of the Orinoco River in Venezuela; the Taíno migrated to Puerto Rico by crossing the Lesser Antilles.

At the time of Columbus' arrival, an estimated 30 to 60 thousand Taíno Amerindians, led by the Agüeybaná, inhabited the island. They called it , "the great land of the valiant and noble Lord". The natives lived in small villages led by a cacique and subsisted on hunting, fishing and gathering of indigenous cassava root and fruit. When the Spaniards arrived in 1493, the Taíno were already in conflict with the raiding Carib, who were moving up the Antilles chain. The Taíno domination of the island was nearing its end, and the Spanish arrival marked the beginning of their believed extinction. However, due to the discovery of pre-contact skeletal remains and subsequent DNA testing, we now know the Taino people live on in their descendants. Their culture, however, remains part of that of contemporary Puerto Rico. Musical instruments such as maracas and güiro, the hammock, and words such as Mayagüez, Arecibo, iguana, Caguas, barbecue (barbacoa) and hurricane (huracán) are examples of the legacy left by the Taíno.

Spanish Empire rule (1508–1898)

Beginning of colonization

On 24 September 1493, Christopher Columbus set sail on his second voyage with 17 ships and 1,200 to 1,500 soldiers from Cádiz. On 19 November 1493, he landed on the island, naming it San Juan Bautista in honor of Saint John the Baptist. The island remained explored and unsettled until the first European settlement, Caparra, was founded on 8 August 1508 by Juan Ponce de León, a lieutenant under Columbus, who was greeted by the Taíno Cacique Agüeybaná and later became the first governor of the island.Vicente Yañez Pinzón is considered the first appointed governor of Puerto Rico, but he never arrived on the island. Ponce de Leon was actively involved in the Hatuey (Jaragua) massacre of 1503 in Haiti on Hispaniola island. In 1508, Ponce de Leon was chosen by the Spanish Crown to lead the conquest and enslaving of the Taíno Indians for gold mining operations. The following year, the colony was abandoned in favor of a nearby islet on the coast, named Puerto Rico (Rich Port), which had a suitable harbor. In 1511, a second settlement, San Germán was established in the southwestern part of the island. During the 1520s, the island took the name of Puerto Rico while the port became San Juan.

The Spanish settlers established the first encomienda system, under which natives were distributed to Spanish officials to be used as slave labor. On 27 December 1512, under pressure from the Roman Catholic Church, Ferdinand II of Aragon issued the Burgos' Laws, which modified the encomienda into a system called repartimento, aimed at ending the exploitation. The laws prohibited the use of any form of punishment toward the indigenous people, regulated their work hours, pay, hygiene, and care, and ordered them to be catechized. But before the laws were promulgated, in 1511 the Taínos revolted against the Spanish; cacique Urayoán, as planned by Agüeybaná II, ordered his warriors to drown the Spanish soldier Diego Salcedo to determine whether the Spaniards were immortal. After drowning Salcedo, they kept watch over his body for three days to confirm his death. The revolt was easily crushed by Ponce de León and within a few decades much of the native population had been decimated by disease, violence, and a high occurrence of suicide. As a result, Taíno culture, language, and traditions were generally destroyed, and were declared to have "vanished" 50 years after Christopher Columbus arrived. Since the early 21st century, efforts have been made to revive and rebuild Taíno culture.

The Roman Catholic Church, realizing the opportunity to expand its influence, also participated in colonizing the island. On 8 August 1511, Pope Julius II established three dioceses in the New World, one in Puerto Rico and two on the island of Hispaniola under the archbishop of Seville. The Canon of Salamanca, Alonso Manso, was appointed bishop of the Puerto Rican diocese. On 26 September 1512, before his arrival on the island, the first school of advanced studies was established by the bishop. Taking possession in 1513, he became the first bishop to arrive in the Americas. Puerto Rico would also become the first ecclesiastical headquarters in the New World during the reign of Pope Leo X and the general headquarters of the Spanish Inquisition in the New World.

As part of the colonization process, African slaves were brought to the island in 1513. Following the decline of the Taíno population, more slaves were brought to Puerto Rico; however, the number of slaves on the island paled in comparison to those in neighboring islands.Dietz, p.38. Also, early in the colonization of Puerto Rico, attempts were made to wrest control of Puerto Rico from Spain. The Caribs, a raiding tribe of the Caribbean, attacked Spanish settlements along the banks of the Daguao and Macao rivers in 1514 and again in 1521 but each time they were repelled by Spanish firepower. However, these would not be the last attempts at control of Puerto Rico. The European powers quickly realized the potential of the newly discovered lands and attempted to gain control of them.

The first school in Spanish-controlled Puerto Rico was the Escuela de Gramatica (Grammar School). The school was established by Bishop Alonso Manso in 1513, in the area where the Cathedral of San Juan was to be constructed. The school was free of charge and the courses taught were Latin language, literature, history, science, art, philosophy, and theology.Hispanic Firsts, by, Nicolas Kanellos, publisher Visible Ink Press; ; p.40

Puerto Rico became a part of New Spain upon its establishment in 1521. The island became a Captaincy General in 1580.

European powers fight over the island

Sparked by the possibility of immense wealth, many European powers made attempts to wrest control of the Americas from Spain in the 16th, 17th and 18th centuries. Success in invasion varied, and ultimately all Spanish opponents failed to maintain permanent control of the island. In 1528, the French, recognizing the strategic value of Puerto Rico, sacked and burned the southwestern town of San Germán. They also destroyed many of the island's first settlements, including Guánica, Sotomayor, Daguao and Loíza before the local militia forced them to retreat. The only settlement that remained was the capital, San Juan. French corsairs would again sack San Germán in 1538 and 1554.

Spain, determined to defend its possession, began the fortification of the inlet of San Juan in the early 16th century. In 1532, construction of the first fortifications began with near the entrance to San Juan Bay. Seven years later the construction of massive defenses around San Juan began, including Fort San Felipe del Morro astride the entrance to San Juan Bay. Later, Fort San Cristóbal and Fortín de San Gerónimo—built with a financial subsidy from the Mexican mines—garrisoned troops and defended against land attacks. In 1587, engineers Juan de Tejada and Juan Bautista Antonelli redesigned Fort San Felipe del Morro; these changes endure.Miller, Paul G. (1947). , 221–237. Politically, Puerto Rico was reorganized in 1580 into a captaincy general to provide for more autonomy and quick administrative responses to military threats.