Archaeological and historical evidence indicate that the Yagua originally inhabited the northern hinterland of the Amazon, the banks of the river being settled by their enemies, the Tupí-speaking Omagua. Only when the latter were weakened by European diseases and intrusions did the Yagua move closer to the main river in order to acquire highly coveted iron goods. The first documented contact with Whites was with the Jesuit Father Samuel Fritz in 1693, when he settled some Pega-Yagua in his missionary station. Until 1768, the date of their expulsion, the Jesuits tried to "settle" the Yagua, mainly on the Amazon or on its main tributaries. They basically failed either because European diseases led the survivors to hide in the inaccessible hinterland or because of Portuguese slave raids on the Spanish missions, but also because of intertribal conflicts with neighboring groups such as the Ticuna, Bora, and Witoto and even between different local Yagua groups. By the nineteenth century, most Yagua had abandoned the riverine settlements and settled again in their homeland.
The situation changed dramatically when rubber extraction reached its peak between 1880 and 1914, and many Indians were deported and forced to work for the rubber gatherers. The Yagua tried to escape the raids by hiding in the least accessible areas. Even there they again were threatened during the Peruvian-Colombian border conflict of 1932-1933. The "conquest of the Amazon" ensued, together with the establishment of extractive activities—lumbering, trade in skins, cattle raising, mining, etc.—that continue today, as does the exploitation of the Yagua and their neighbors as cheap labor. The contractors or patrones (sing., patrón; anyone who buys the services of others by advancing them goods or credit) have achieved over the last fifty years what the missionaries failed to do—the settlement of the majority of the Yagua on the Amazon.