The Manco Inca dynasty resisted the Spanish conquerors during 40 years (1 536 to 1 572) from this fortress in the Vilcabamaba area. The Spanish conquerors were never able to expel them from it.

The building of Chocquequirao is the work of Inca Pachacutec successors Tupac Inca Yupanqui (1 471-1 493) and Wayna Capac (1 493-1 527). Household and ceremonial pottery has been found here that bears both the classic Cusco style and also from other populations who came to live here to build and permanently populate the area. Most likely, they were experienced farmers who knew how to build and use farming terraces in high Amazon forest areas. Located at 3 050 masl on the border with department of Apurímac, the Choquequirao archeological compound was not built to be a place of easy access. Reaching it demands two days of disciplined march, largely compensated by the beauty of the landscape that wayfarers cross from the beginning of their expedition.

The road starts at Cachora (2 300 masl), a small town in the Apurímac department, after traveling four hours on the mostly paved road from Cusco (145 km paved and 10 km of dirt road). Mule packers can be contacted there who can also act as guides. A local family offers accommodation and the only telephone in town. Approximately 40% of the Choquequirao Inca ceremonial center has been cleared of vegetation. The remaining area is formed by a complex terrace system built on extremely steep slopes. A very impressive stairway of 180 terraces has been recently spotted. It descends from one of the ceremonial center flanks and reaches the river open to swimming.

Choquequirao was probably one of the entrance check point to the Vilcabamba region, and also an administrative hub serving political, social and economic functions. Its urban design has followed the symbolic patterns of the imperial capital, with ritual places dedicated to the Sun (Inti) and the ancestors, to the earth, water and other divinities, with mansions for administrators and houses for artisans, warehouses, large dormitories or kallankas and farming terraces belonging to the Inca or the local people. Spreading over 700 meters, the ceremonial area drops as much as 65 meters from the elevated areas to the main square.