According to the BBC, you can find evidence for a pre-Incan society, the Killke culture, in and around Cuzco--most notably in the periphery of the Sacsayhuaman temple. This culture dates from around A.D. 900 to A.D. 1200.
Legends claim that Inti, the son god, ordered his son Manco Capac to find the "naval of the Earth" or "qosq'o" in Quechua, the native language. Incan cultures moved into the Cuzco area in the early 12th century A.D.
Atahualpa and his brother Huascar fought over control of the Cuzco area prior to the arrival of the Spaniards, thus weakening the unified front of the Inca against the Spaniards. Although rightfully under control of Huascar, Atahualpa won Cuzco in 1532.
Francisco Pizarro and the Spanish rode into Cuzco in November 1533. After fierce battles, the Spaniards captured and ultimately killed Atahualpa. The Spaniards, with some difficulty, took control of Cuzco.
Following Pizarro's arrival, there were several uprisings that were later subdued. Despite all of this, Cuzco remained a small country city until the rediscovery of Machu Picchu in 1911, which turned this entire region into a tourist mecca.
