The Killke people occupied the region from 900 to 1200, prior to the arrival of the Inca in the 13th century. Carbon-14 dating of Saksaywaman, the walled complex outside Cusco, has established that the Killke culture constructed the fortress about 1100. The Inca later expanded and occupied the complex in the 13th century and after. On 13 March 2008, archaeologists discovered the ruins of an ancient temple, roadway and aqueduct system at Saksaywaman. The temple covers some 2,700 square feet (250 square meters) and contains 11 rooms thought to have held idols and mummies, establishing its religious purpose. Together with the results of excavations in 2007, when another temple was found at the edge of the fortress, indicates there was longtime religious as well as military use of the facility, overturning previous conclusions about the site.
See also: Kingdom of Cusco and Inca Empire
Cusco has long been an important center of indigenous peoples. It was the capital of the Inca Empire (13th century-1532). Many believe that the city was planned as an effigy in the shape of a puma, a sacred animal. It is unknown how Cusco was specifically built, or how its large stones were quarried and transported to the site. Under the Inca, the city had two sectors: the urin and hanan. Each was divided to encompass two of the four provinces, Chinchasuyu (NW), Antisuyu (NE), Kuntisuyu (SW) and Qullasuyu (SE). A road led from each of these quarters to the corresponding quarter of the empire.
Each local leader was required to build a house in the city and live part of the year in Cusco, restricted to the quarter that corresponded to the quarter of the empire in which he had territory. After the rule of Pachacuti, when an Inca died, his title went to one son and his property was given to a corporation controlled by his other relatives (the process was called split inheritance). Each title holder had to build a new house and add new lands to the empire, in order to own the land his family would to maintain after his death.
According to Inca legend, the city was rebuilt by Sapa Inca Pachacuti, the man who transformed the Kingdom of Cuzco from a sleepy city-state into the vast empire of Tawantinsuyu. Archaeological evidence, however, points to a slower, more organic growth of the city beginning before Pachacuti. The city was constructed according to a definite plan, and two rivers were channeled around the city. Archaeologists such as Larry Coben have suggested that this city plan was replicated at other sites throughout the empire.
The city fell to the sphere of Huáscar during the Inca Civil War after the death of Huayna Capac in 1527. It was captured by the generals of Atahualpa in April 1532 in the Battle of Quipaipan. Nineteen months later, Spanish explorers invaded the city (see battle of Cuzco) and gained control because of their arms and horses, comprising a superior military technology.
The first three Spaniards arrived in the city in May 1533, after the Battle of Cajamarca, collecting for Atahualpa's Ransom Room. On 15 November 1533. Francisco Pizarro officially arrived in Cusco. "The capital of the Incas...astonished the Spaniards by the beauty of its edifices, the length and regularity of its streets" The great square was surrounded by several palaces, since "each sovereign built a new palace for himself." "The delicacy of the stone work excelled" that of the Spaniards'. The fortress had three parapets, and was composed of "heavy masses of rock." "Through the heart of the capital ran a river...faced with stone." "The most sumptuous edifice in Cuzco...was undoubtedly the great temple dedicated to the Sun...studded with gold plates...surrounded by convents and dormitories for the priests." "The palaces were numerous, and the troops lost no time in plundering them of their contents, as well as despoiling the religious edifices," including the royal mummies in the Coricancha.
Pizarro ceremoniously gave Manco Inca the Incan fringe as the new Peruvian leader. Pizarro encouraged some of his men to stay and settle in the city, giving out repartimientos to do so. Alcaldes were established and regidores on 24 March 1534, which included his brothers Gonzalo Pizarro and Juan Pizarro. Pizarro left a garrison of 90 men and then departed for Jauja with Manco Inca.
Pizarro renamed it the "Very noble and great city of Cuzco". The many buildings constructed after the Spanish invasion have a mixture of Spanish influence with Inca indigenous architecture, including the Santa Clara and San Blas neighborhoods. The Spanish destroyed many Inca buildings, temples and palaces. They used the remaining walls as bases for the construction of a new city.
Father Vincente de Valverde became the Bishop of Cusco, and built his cathedral facing the plaza, placed a St. Dominic monastery on the ruins of the House of the Sun, and a nunnery where the House of the Virgins of the Sun was stood.
The city was retaken from the Spanish during the Siege of Cuzco of 1536 by Manco Inca Yupanqui, a leader of the Sapa Inca. Although the siege lasted 10 months, it was ultimately unsuccessful. Manco's forces were able to reclaim the city for only a few days. He eventually retreated to Vilcabamba, the capital of the newly established small Neo-Inca State, which lasted for another 36 years but he was never able to return to Cuzco. Throughout the conflict and years of the Spanish colonization of the Americas, many of Inca citizens and warriors succumbed to smallpox and died.
Cusco stands on layers of cultures, with the Tawantinsuyu (old Inca Empire) built on Killke structures, and the Spanish having replaced indigenous temples with Catholic churches, and palaces with mansions for the invaders.
Cusco was the center for the Spanish colonization and spread of Christianity in the Andean world. It became very prosperous thanks to agriculture, cattle raising, and mining, as well as its trade with Spain. The Spanish colonists constructed many churches and convents, as well as a cathedral, university and Archbishopric. Just as the Inca built on top of Killke structures, Spanish buildings were based on the massive stone walls built by the Inca.
A major earthquake on 21 May 1950 caused severe localised damage in Cusco. The Dominican Priory and Church of Santo Domingo, which were built on top of the impressive Qurikancha (Temple of the Sun), were among the affected colonial era buildings. However, the city's Inca architecture withstood the earthquake. Many of the old Inca walls were at first thought to have been lost after the earthquake, but the granite retaining walls of the Qurikancha were exposed, as well as those of other ancient structures throughout the city. Restoration work at the Santo Domingo complex was conducted in such a way as to expose the Inca masonry formerly obscured by the super-structure without compromising the integrity of the colonial heritage.