According to studies and archeological discoveries, the origins of the first inhabitants go back to the year 8060 BC in the Cave of Chopsi. They were hunters, hunting everything the Páramo offered them, and nomads, following the animals and seasons. Their culture is represented by tools such as arrows and spears, which have been found throughout the Andean valley. The culture was most present about 5585 BC.
Later the early indigenous people used the stable climate, fertile soil and abundant water to develop agriculture. They grew potatoes, melloco, chocho, squash and quinoa. They also domesticated animals such as cuys (guinea pigs) and camelids: llamas and alpacas.
Their technology was also advanced. For example, they started creating ceramics. In fact, ceramics constitute the greatest number of artifacts which archeologists use to study their culture. The period from 5000 BCE to 2000 BCE is not represented well in the archeological record. Beginning around 2000 BCE, the people developed a more highly organized society, demonstrating delegated responsibilities, such as the managing of water and control of plagues. People were specialized as administrative and religious authorities (known as shamans). This occurred during the periods of Chaullabamba, Huayco, Pirincay, Monjas, Putushio, Huancarcucho and Jubones. From then until 500 AD began the periods of Tacalshapa III and the Cañari people, who were absorbed into the Incas in the 15th century.
Cuenca was originally a Cañari settlement called Guapondeleg. Archeologists believe Cuenca was founded around 500 AD. Guapondeleg translates into "land as big as heaven." Less than half a century before the conquistadors landed, the Incas, after a bitter struggle, conquered the Cañari and occupied Guapondeleg and the surrounding area. Though the Incas replaced the Cañari architecture with their own, they did not suppress the Cañari or their impressive achievements in astronomy and agriculture. As was customary for the Incas, they absorbed useful achievements into their culture. They renamed the city Tomebamba. The city became known as the second Cusco, a regional capital.
After the defeat of the Cañari, probably in the 1470s, the Inca emperor, Tupac Yupanqui, ordered the construction of a grand city to be called Pumapungo, "the door of the Puma". Its magnificence was said to have rivaled that of the Inca capital of Cuzco. Indians told stories to the Spanish chroniclers of golden temples and other such wonders, but by the time the Spaniards found the legendary city, all that remained were ruins. They wondered what happened to the fabled splendor and riches of the second Inca capital. After having been abandoned by the Cañari and then the Incas, Tomebamba was sparsely populated until the 1550s.
Tomebamba is considered a candidate for the mythical city of gold which the Spanish called El Dorado. The Spanish thought El Dorado was burned by the inhabitants after they heard of the Spanish conquests. Tomebamba's destruction by its inhabitants prior to the arrival of the Spanish suggests it may have been what the Spanish called El Dorado.
The Spanish settlement of Cuenca was founded on April 12, 1557 by the explorer Gil Ramírez Dávalos. Andrés Hurtado de Mendoza, then Viceroy of Peru had commissioned the founding and ordered the city named after his home town of Cuenca, Spain. It was founded decades after other major Spanish settlements in the region, such as Quito Guayaquil (1538), and Loja (1548).
Cuenca's population and importance grew steadily during the colonial era. It reached the peak of its importance in the first years of Ecuador's independence; Cuenca achieved its independence on November 3, 1820. It became the capital of one of the three provinces that made up the nascent republic. The other two capitals were Guayaquil and Quito.