The earliest evidence of human presence in Ecuador was discovered east of Quito at the El Inga archeological site and dates back to 10,000 BC, when small hunter-gatherer communities collected seeds, berries, roots, insects and reptile eggs from the valley forests and roamed the high grasslands for bigger game. The set of arrowheads and spear points found here were carved from glassy black obsidian and basalt, materials taken from the huge lava wastes that then scarred the Andes; similar fragments made with hard volcanic materials have been recovered from the Loja and Azuay areas in the southern sierra. On the coast at about this time, other hunter-gatherer groups of the Las Vegas culture were emerging around the Santa Elena peninsula, and by 6000 BC they were beginning seasonal cultivation of food crops and cotton - Ecuador's first known agriculturists .

Certain characteristics of Las Vegas culture, such as the repeated use of certain settlements and the fashioning of basic tools from polished stone, laid the basis for the Valdivia culture, which blossomed around 3500 BC and spread across the coast to southern Esmeraldas and El Oro over the next two thousand years, dominating the early Formative Period (4000-400 BC). The Valdivia culture is best known for its ceramics - among the oldest found in South America - especially their "Venus figurines", highly stylized miniatures of women with long, flowing hair and often pregnant, which are believed to have been part of a fertility cult. They lived in oval, wood and thatch houses surrounding a central square, in permanent villages strung along the coast and around river plains, where the soil was fertile enough to grow maize, cotton, cassava, peppers and kidney beans.

In contrast to this, the Machalilla culture (1500-800 BC) that followed them, preferred rectangular structures on stilts, and practised skull deformation as a sign of status. They were more expert than their Valdivia counterparts at fishing and had surplus stores for trading with neighbouring groups. Their ceramic flasks, characterized by circular or "stirrup-shaped" spouts are similar to those made by the Cotocollao, Cerro Narrío and Upano cultures, suggesting there was contact between them. Based around the Quito area, the Cotocollao people traded agricultural produce such as quinoa for coastal cotton, while the Cerro Narrío site in the southern sierra was an important trading centre between the coast and the Upano group based around Volcán Sangay in the upper Amazon basin. This communication across the regions seems to have intensified with the Chorrera culture (900-300 BC), which flourished on the coast at the close of the Formative Period, a sophisticated people that crafted some of the most beautiful ceramics of that age, distinctive for their iridescent sheen.

The subsequent Regional Development Period (300 BC-800 AD) saw a splintering of cultures and the appearance of some highly stratified societies. The driving force behind these changes seems to have been a burgeoning economy and related interaction between cultures, as each sought the goods and resources needed to support an increasingly complex social organization. As trading routes sprang up along the coast, seafaring cultures, such as Bahía (from south of Bahía de Caráquez, dating to 500 BC-650 AD), Jama-Coaque (north of Bahía, from 350 BC to 1540 AD) and Guangala (Guayas coast from 100 BC to 800 AD), transported their wares on balsa-wood rafts with cotton sails. The merchants of these cultures took on an elite status alongside their religious orders, in effect acting as diplomats for their group, who ensured a supply of necessary goods from neighbouring tribes. The merchants' most treasured possession, above even gold and platinum, was the deep-crimson spondylus (thorny oyster) shell, harvested from a depth of twenty to sixty metres by highly skilled fishermen. Prized ornaments and religious symbols of fertility, the shells were also a kind of universal currency, exchanged for anything from animal furs and armadillo shells to colourful cloths and beeswax. Such was the range of these traders that ceramics representing them - through " basketmen " motifs, sitting figures often adorned with necklaces, bracelets, earrings, with outsized baskets on their backs - have been found on the Pacific coast from Ecuador to Central America.

Meanwhile, in northern Esmeraldas and stretching into Colombia, the culture of La Tolita held one of the prime religious and trading centres on the South American coast, thought to have been at the island of La Tolita, in the mangroves near San Lorenzo. Traders, craftsmen and worshippers from different regions swarmed to the site and the intense cross-fertilization of ideas led to creation of exquisite ceramic styling and most famously, metalwork, including fine objects of platinum, silver, copper and gold.

The final stage before the arrival of the Incas is known as Integration (800-1480 AD), when political leaders and chiefs ( curacas ) of local territories defined through frequent skirmishes, exacted tributes and levied taxes from their communities. Agricultural productivity surged through improved techniques in irrigation and terracing, and trading continued to boom. On the coast the Manteño-Huancavilca culture (500 BC-1540 AD), occupying land from the Gulf of Guayaquil to Bahía de Caráquez, continued the seafaring traditions of their coastal forebears, while also producing distinctive artefacts, such as the ceremonial U-shaped chairs supported by human or animal figures, and black ceramics. To their north, people such as the Nigua, Chachi, Campaz, Caraque and Malaba continued to live by hunting, fishing and farming small agricultural plots. Inland, to the south, the Chono - the ancestors of the Tsáchila (or Colorados) of today, defined archeologically as the Milagro-Quevedo culture - were known for fine weavings and gold adornments such as noserings, headbands and breastplates. They also frequently warred with the fierce Puná , who occupied the island of the same name in the Gulf of Guayaquil.

In the highlands at this time, the major population groups occupied the elevated valley basins between the western and eastern cordilleras of the Andes, each basin ( hoya ) separated from the next by mountainous nudos , "knots" where the cordilleras tie together. From north to south were: the Pasto , occupying southern Colombia and Carchi; the Cara (or Caranqui), living around Ibarra, Otavalo and Cayambe, and responsible for enormous ceremonial centres such as the one at Cochasquí; the Panzaleo (also called the Quito), who inhabited the Quito valley, Cotopaxi and Tungarahua, and did much trade with the Quijo in the Oriente; the Puruhá , of the Chimborazo region; the Cañari , great gold and copper craftspeople who dominated the southern sierra; and the Palta , a tribe whose major centre was Saraguro near Loja and who had strong links with the Amazonian group, the Shuar .