Puno and the Lake Titicaca region have a long (and violent) history. Beginning around 1000 BC, the Qaluyu culture was the primary group inhabiting in the area. They were dominant until around 200 AD and the Tiahuanaco culture gained prominence in the Puno area and the Qaluyu culture subsequently declined.
The Inca civilization began to assert itself in the Puno region during the 15th century. Inca mythology asserts that Inca Manco Capac and his sister Mama Occla rose out of Lake Titicaca's waters with the divine purpose of creating and uniting a kingdom of peace and civilization. Puno and Lake Titicaca gained increased importance to the Incas because of the plethora of silver and gold in the area. Additionally, the Incas raised alpacas and llamas for wool and meat and cultivated high-altitude crops such as potatoes and coffee.
The Spanish arrived in Puno in 1534, led by Francisco Pizarro. Initially, colonization went relatively smoothly for the Conquistadors. Within the century, the presence of precious metals caused an increase in fighting, especially over the silver and gold rich Laykakota Mines west of Puno. In the 1660s the fighting reached such a level that the Spanish viceroy at the time, Viceroy Conde de Lemos, arrived to quell the situation with drastic measures. He closed the mine, executed the one of the owners (probably the richest man in Latin America at the time), burned down the town that had grown up around it and founded Puno eight kilometers down the road. The exact location of the mines still remains a mystery today.
Fighting again erupted in Puno in the 1780s when indigenous communities began fighting for independence. They continued until 1821 when Peru was granted independence.
At this point Bolivia filled the void left by the Spanish and Puno became one site of the territory war between Peru and Bolivia. The warring between the two countries continued until 1847 when the countries agreed on boundaries and the fighting stopped.