Linguistic analysis suggests a split of the Tukanoan Language Family into Eastern and Western Branches about 1,500 to 2,000 years ago. The Eastern Tukanoan area centers on the Río Vaupés of eastern Colombia and northwest Brazil and includes cultures such as the Cubeo, the Desana, and the Tukano. The Western Tukanoan area is located approximately 600 kilometers to the southwest in the Napo and Putumayo drainages. Witoto (Tupí Language Family) and Carijona (Carib Language Family) groups occupy the lands separating the Eastern and Western Tukonoans.
In the seventeenth and eighteenth centuries Jesuit missionaries referred to the Western Tukanoans of the Aguarico-Napo area as the "Encabellado" because of their long hair. Native groups bordering the Encabellado territory at that time included the Kofán (Cofán) to the west, the Záparo and the Awishira to the south, the Coto or Orejón (also Western Tukanoan) to the east, and the Witoto to the north. Relations among various Encabellado groups were brittle because of accusations of sorcery, which occasionally led to raiding. The principal enemies of the Encabellado, however, were the Awishira, who lived in forests south of the Río Napo. These two groups attacked each other back and forth across the Napo. The Encabellado were visited by Jesuit missionaries in 1599. In 1638—1639 the Portuguese expedition of Captain Pedro Teixeira was attacked by the Encabellado residing near the confluence of the Aguarico and Napo, and the Portuguese burned several native settlements in reprisal.
In 1683 a royal decree gave the Jesuits the authority to missionize the natives of the Napo and Aguarico rivers and the Franciscans authority over the Putumayo. The period from 1709 to 1769 saw much Jesuit activity—seventeen missions were founded in the Aguarico-Napo region. The strategy was to take the natives from their dispersed settlements in the forest and concentrate them in larger villages or "reductions" along the banks of the major rivers. The new missions proved unstable, as people left them to go foraging or abandoned them whenever illness or accusations of sorcery arose. In 1744 a native named Curazaba killed Padre Francisco Real and two assistants at San Miguel. Shortly thereafter, the Encabellado abandoned eight missions. In 1767 King Charles III ordered the Jesuits expelled from Spain's New World colonies, and their missions died out.
The records of the nineteenth century are limited to the accounts of a few travelers, who now referred to the natives as the "Santa María," "Angutera," and "Piojé." These Indians bartered with river traders, exchanging forest products and hammocks for iron tools, cloth, and manufactured items. In the early twentieth century some settlements fell under the control of White patrones who exploited native labor to collect forest products and grow crops. By this time, epidemic diseases had greatly reduced the Western Tukanoan population. In 1941 Peru invaded Ecuador along the Río Napo, and the de facto boundary established at Pantoja bisected the scattered Western Tukanoan population. In the latter part of the twentieth century, Siona in Colombia live in small settlements along the Río Putumayo and its tributary, the Rio San Miguel. In Ecuador, Siona and mixed Siona-Secoya communities are located along the Rio Aguarico and its tributaries, the Eno and Cuyabeno. In Peru, Secoya and Angotero settlements are located on the Angusilla, Santa Maria, and Yubineto rivers.