The discovery and conquest of Ecuador by Spanish forces in the early sixteenth century are adjuncts to the history of the conquest of Peru, the richest of the New World prizes won for the Spanish crown. The central figure of that history is Pizarro, an illiterate adventurer from Trujillo in the Spanish region of Extremadura, who had accompanied Vasco Núñez de Balboa in his crossing of the Isthmus of Panama to discover the Pacific in 1513. Eleven years later, Panamanian governor Pedro Arias de Avila ("Pedrarias") authorized Pizarro, in partnership with an equally questionable character, a Castilian named Diego de Almargo, and a priest named Fernando de Luque, financing to explore southward down the west coast of South America. Their first two voyages, in 1524 and 1526, ended in failure; not until the third voyage, launched in 1531, would the Peruvian prize be won and the Inca be conquered.

The first European to set foot on the territory of modern-day Ecuador was probably Bartolomé Ruiz de Estrada, the pilot for Pizarro on his second voyage, who pushed southward while Pizarro explored the Colombian coast and Almargo returned to Panama for supplies. Pizarro himself landed on the Ecuadorian coast later during his exploratory voyage and traveled as far as Tumbes in the extreme north of present-day Peru, in defiance of official orders to return to Panama.

Having thus lost the favor of the king's representatives in Panama, Pizarro was forced to return to the royal court in Spain to petition King Charles I personally for authorization of a third voyage. Flush with the success of Hernán Cortés in Mexico and tantalized by the gold pieces brought by Pizarro from Tumbes and growing fables of great wealth in the South American interior, Charles granted Pizarro authorization and much more: the titles of governor and captain-general of Peru, a generous salary, and extensive territorial concessions. Almargo was granted important, although less generous, titles and privileges; his resentment of this slight would affect relationships for the rest of the conquest. At the time that Charles granted various titles to Pizarro and Almargo, he named de Luque Bishop of Tumbes. Before returning to Panama in 1530, Pizarro recruited for the conquest several immediate family members, including two full brothers named Gonzalo and Juan as well as two half-brothers. The participation of so many of Pizarro's relatives further strained relations between the two partners in conquest.

Pizarro then embarked from Panama with some 180 men while Almargo remained there to gather additional recruits. After thirteen days at sea, Pizarro landed once again on the coast of Ecuador, where he procured some gold, silver, and emeralds, which were dispatched to Panama and put to good use in Almargo's efforts. Although the capture of the Inca stronghold of Tumbes was Pizarro's first objective, he was forced to spend several months in Ecuador, first nursing a rash of ulcers and then fighting the fierce warriors of the island of Puná. By the time the conquerors arrived in Tumbes, it had been destroyed by the Puná warriors and its population dispersed. Just to the south, they founded the first Spanish settlement in Peru, San Miguel de Tangarará. Upon their fateful departure to Cajamarca on September 24, 1532, Pizarro left a lieutenant, Sebastián de Benalcázar, in charge of protecting and developing San Miguel as a Spanish base of operations. Two years later, Benalcázar would lead the conquering forces that moved northward into Ecuador.

Meanwhile, Atahualpa was resting near Cajamarca, in the Sierra of northern Peru, following the defeat and capture of his brother. He had known of the arrival of foreign invaders for several months; it is not clear why he did not order their obliteration before they could penetrate into the heart of the empire. After a march of almost two months, Pizarro arrived in Cajamarca and summoned Atahualpa from the nearby thermal baths known today as the Baños del Inca. Reluctantly, accompanied by several thousands of his best troops, Atahualpa went to Cajamarca's central plaza, where he was met, not by the conquistadors, but by their chaplain, Fray Vicente de Valverde, who called upon the Inca emperor to submit to the representatives of the Spanish crown and the Christian god. Atahualpa replied disparagingly and, upon his throwing a Christian prayer book to the ground in contempt, concealed Spanish soldiers opened fire, killing thousands of Atahualpa's defenders and taking the Inca emperor captive. This slaughter, called "the decisive battle" of the conquest of Peru by historian Hubert Herring, took place on November 16, 1532.

A panic-stricken Atahualpa, fearing that Pizarro might be planning to depose him in favor of his rival brother, summoned Huascar, at this time imprisoned in Cuzco, to Cajamarca, then ordered him to be executed along with hundreds of Huascar's nearest of kin. It served the Spaniards' purposes to allow Atahualpa the freedom, from his cell, to command his forces. Thus continued the rapid annihilation, through a vicious civil war that now overlapped with the Spanish conquest, of the army and leadership of one of the great polities of modern history. Pizarro was not planning to depose Atahualpa, of course, but to execute him. First, however, he had Atahualpa fill his cell, once with gold, then twice with silver (estimated at 4,850 kilograms of gold and 9,700 kilograms of silver) supposedly as ransom for his release. Instead the Spaniards garrotted Atahualpa on August 29, 1533, following a mock trial at which he was convicted of every charge that Pizarro could invent for the occasion. Having deprived the Inca empire of leadership, Pizarro and another conquistador, Hernando de Soto, moved south to Cuzco, the heart of Tawantinsuyu, which they captured in November 1533; they then led their men in an orgy of looting, pillaging, and torture in search of more precious metals.

Benalcázar, Pizarro's lieutenant and fellow Extremaduran, had already departed from San Miguel with 140 foot soldiers and a few horses on his conquering mission to Ecuador. At the foot of Mount Chimborazo, near the modern city of Riobamba, he met and defeated the forces of the great Inca warrior Rumiñahui with the aid of Cañari tribesmen who, happy to throw off the yoke of their Inca rulers, served as guides and allies to the conquering Spaniards. Rumiñahui fell back to Quito, and, while in pursuit of the Inca army, Benalcázar encountered another, quite sizable, conquering party led by Guatemalan Governor Pedro de Alvarado. Bored with administering Central America, Alvarado had set sail for the south without the crown's authorization, landed on the Ecuadorian coast, and marched inland to the Sierra. Pizarro had heard of this competing expedition some time earlier and had sent Almargo north to reinforce Benalcázar. Together, Pizarro's two representatives managed to convince Alvarado, with the help of a handsome amount of gold, to call off his expedition and allow the "legal" conquest to proceed as planned. Most of Alvarado's men joined Benalcázar for the siege of Quito.

Rumiñahui left Quito in flames for the approaching conquistadors. It was mid-1534 and, after the customary orgy of violence, in December the Spanish established the city of San Francisco de Quito on top of the ruins of the secondary Inca capital. Benalcázar was soon off on more conquests in Colombia to the north; it was not until December 1540 that Quito received its first captain-general in the person of Gonzalo Pizarro, the brother of Francisco.

Benalcázar had also founded the city of Guayaquil in 1533, but it had subsequently been retaken by the local Huancavilca tribesmen. Francisco de Orellana, yet another lieutenant of Francisco Pizarro from the Spanish city of Trujillo, put down the native rebellion and in 1537 reestablished this city, which a century later would become one of Spain's principal ports in South America.

Orellana is chiefly remembered, however, for being the first European to travel the length of the Amazon River. This journey, one of the great adventure tales of Spain's conquest of America, began in February 1541, when the lure of spices, particularly cinnamon, led Pizarro's brother Gonzalo to set off from Quito to the eastern jungle with a party that included 210 Spaniards and some 4,000 Indians. Orellana was second in command. After several months of hardship and deprivation during a crossing of the Cordillera Oriental of the Andes that cost the lives of nearly half the party, Gonzalo Pizarro placed Orellana in charge of building a brigantine in the Coca River in present-day Ecuador. Together with fifty-seven Spaniards and several hundred Indians, Orellana sailed downstream in search of food and friendly natives. The explorers never rejoined Pizarro, however, but set out on their own in search of neither food nor spices, but gold. "Having eaten our shoes and saddles boiled with a few herbs," wrote Orellana in a caricature of the ruggedness for which the Extremaduran conquerors were noted, "we set out to reach the Kingdom of Gold." The group reached the mouth of the Amazon, a name given by Orellana because he believed that they had been attacked by the legendary giant female warriors at a point below the Negro River, and sailed northward along the Atlantic coast as far as Venezuela, then back to Spain. The journey completed by the expedition headed by Orellana was not to be repeated for 100 years.

In the same August 1542, as Orellana reached the Atlantic, Gonzalo Pizarro was stumbling back to Quito with the few surviving members of his party. He found Peru in political chaos. Several years earlier, Almargo had entered into open rebellion against Francisco Pizarro and been defeated in battle, tried, and executed in his newly founded capital city of Lima. The resentment among Almargo's followers did not end, however, and in June 1541, Francisco Pizarro had been assassinated by the remnants of Almargo's army. In an attempt to try to control the unruly conquistadors and to end the enslavement of the native population of America, the Spanish crown had promulgated the New Laws in 1542, which in theory though not in practice abolished encomiendas, and two years later it sent its first viceroy to head a newly created colonial administrative system.

Gonzalo, who had little interest in being controlled by anyone, defeated and killed the first viceroy on a battlefield near Quito. After a brief period of glory, however, the younger Pizarro was himself defeated by the forces of a subsequent royal emissary, and in 1548 he was tried and hung for treason. It was the end of the tumultuous era of the conquistadors and the beginning of two and a half centuries of relatively pacific colonial rule.

Data as of 1989