There is much unknown about the site, Choquequirao still reveals its mysteries to archaeologists today. Ceramic studies demonstrate that the area where Choquequirao stands was inhabited long time before the incas.
Along the Vilcanota and Vilcabamba rivers, the Incas went into the jungle to establish specialized production centers of coca, precious metals, bird feathers, dyes and other luxury goods destined to the Inca elite. The construction of Choquequirao and the network of roads that connected it with Machu Picchu, Vitcos and Vilcabamba had to respond to a complementation with these purposes.
We presume that the Inca government built Choquequirao for religious and pilgrimage purposes, a sanctuary linked to the tutelary “Apus” (Gods) of this part of the "sierra nevada", without ceasing to suppose that this great work had the purpose of perpetuating the memory of the power of its Ruler builder.
Either Tupac Yupanqui or Huayna Capac (XV and XVI centuries) built the impressive citadel on that location as well as a complete trail system that connected with Machu Picchu, Vilcabamba and the central site of Vitcos (capital of the last Incas).
The story of the last Inca rulers or “The Vilcabamba Incas” starts with Manco Inca’s failed siege of Cusco. He escaped to Ollantaytambo in the Sacred Valley and then went north to the heart of the Vilcabamba Mountain Range. The rebellion only ended 36 years later, when Tupac Amaru I was executed in Cusco’s Main Square, in 1572.
The Inca cities built within the Vilcabamba mountains were slowly reclaimed by the jungle and forgotten by the people.
News of Choquequirao were heard in 1710 and french explorer Eugene De Sartiges got to the site in 1834. Bingham reached Choquequirao in 1909 and pressed on to Machu Picchu in 1911, claiming the latter as the “Lost City of the Incas”. Most scholars agree that Espiritu Pampa (“Plain of Ghosts” or “Vilcabamba the Old”, also discovered by Bingham and then studied by Savoy) is the last city of the rebel Incas of Vilcabamba.
Choquequirao was once again forgotten until 1968 when the sanctuary was included in the Official Register of Archeological Monuments by Peruvian authorities.