A state that did not end in 1532
The capture of Atahualpa at Cajamarca is often presented as the end of the Inca Empire, but the state survived in some form for four more decades. The story has three parts: a civil war that split the empire, an epidemic that may have helped to cause it, and a smaller Inca state in the mountains and forests of Vilcabamba that kept Spanish rule from being complete until 1572. The central events are well documented in Spanish and Inca-descended sources, though many details and numbers remain uncertain.
Epidemic disease before the Spanish
Old World diseases reached the Andes ahead of the conquerors. According to Spanish writers, a serious epidemic swept through Inca territory in the mid-1520s, and the ruler Huayna Capac died around 1527, probably from the same outbreak or a related one. His chosen heir is also said to have died. Smallpox is the disease most often named, but the evidence is indirect, because the descriptions are brief and written later, and scholars debate which illnesses were involved. Estimates of how many people died vary widely, and no reliable figure exists.
Even so, historians generally agree that disease was a major shock. Andean communities had no previous exposure to the pathogens. The epidemic removed or weakened key figures at a sensitive moment and complicated the transfer of power.
Huascar and Atahualpa
Huayna Capac did not leave a clear successor. His sons Huascar and Atahualpa came from different mothers and had different bases of support. Huascar was recognised in Cuzco, which gave him the backing of much of the old nobility. Atahualpa was in the north, where Huayna Capac had spent long years campaigning, and he commanded veteran troops led by generals such as Quisquis and Chalcuchima.
Open conflict began around the late 1520s. The accounts describe a series of battles moving from the north toward Cuzco, with heavy casualties. Atahualpa’s forces won most of the major engagements, and around 1532 they defeated Huascar’s army near Cuzco and captured him. Many of the details, including exact dates and numbers, come from later writers with their own loyalties, so they should be treated cautiously. What matters is that the empire was recently divided, with grievances on both sides and a large army still in the field when Pizarro arrived.
The Spanish exploited these divisions. At Cajamarca, they captured Atahualpa, who was killed in 1533 after the payment of a ransom. The meeting of Pizarro and Atahualpa has been retold many times; the key consequence here is that the Spanish now had no strong Inca ruler to deal with, and they chose to install a more pliable one.
Manco Inca’s rebellion
The Spanish selected Manco Inca, a brother of Huascar, as ruler in Cuzco in 1533. He soon found that the Spanish treated him as a puppet and abused his people and relatives. In 1536 he escaped and raised a large army. His forces laid siege to Cuzco for months and came close to retaking the city, occupying the fortress of Sacsayhuaman for a time before the Spanish regained it. The siege failed in part because of the Spanish cavalry, in part because Indigenous allies fought on the Spanish side, and in part because the Inca army could not be kept in the field during the farming season.
Manco withdrew first to Ollantaytambo, where his forces won a notable victory in 1537, and then deeper into the mountains. From about 1539 he established himself in the Vilcabamba region, a rugged zone of high ridges and cloud forest north-west of Cuzco, reachable by only a few difficult routes. There he ruled a smaller Inca court that continued rituals and kept the Inca royal line alive. He was killed in 1544 by Spanish men who had been sheltering with him as fugitives from a Spanish internal conflict.
Negotiation and the last years
Manco’s sons ruled in turn. Sayri Tupac negotiated with the Spanish authorities and left Vilcabamba in 1558 to receive an estate in the Yucay valley, dying a few years later. His brother Titu Cusi then ruled from about 1560. He maintained the independence of the Vilcabamba state while dealing with the Spanish, and in 1566 he agreed to the Treaty of Acobamba. He allowed a few Spanish missionaries into his territory. Titu Cusi also dictated an account of the conquest from the Inca point of view, which survives and is an important source, though it was shaped by his political aims.
Titu Cusi died in 1571, and the death of a Spanish priest at about the same time gave the viceroy, Francisco de Toledo, a reason to act. His expedition entered Vilcabamba in 1572, and the Inca capital there was taken. Titu Cusi’s brother Tupac Amaru, the last ruler, was captured in the forest and brought to Cuzco, where he was executed in September 1572. With his death, the Inca royal line ceased to rule any independent territory.
Where was Vilcabamba?
The location of the rebel capital has long attracted interest. In 1911 the explorer Hiram Bingham reached Machu Picchu and initially believed it might be the “lost city” of the last Incas, an idea that fed popular Machu Picchu secrets stories. Later research showed Machu Picchu was not Vilcabamba. The site of Espiritu Pampa, deep in the forest, is now widely identified with the final Inca capital, though archaeologists continue to refine the picture.
Resistance elsewhere in the Americas
Long resistance was not unique to the Inca. In Mesoamerica, the Spanish conquest of Yucatan took decades, and the last independent Maya kingdom, centred on the Itza, held out until 1697. The Aztec capital, by contrast, fell within about two years of the Spanish landing, in the events of Cortes and Tenochtitlan. In every case, the speed of conquest depended on local politics, geography, disease and Indigenous alliances as well as on Spanish arms.
The Inca experience also shows that the end of a state is not the end of a people. After 1572, Quechua-speaking communities continued under colonial rule, and later Andean uprisings, such as the large rebellion of Tupac Amaru II in 1780, drew on the memory of the Inca past. Descendants of the Inca and their subjects remain a large part of the population of the Andes today.