Archaeological data from the area indicate continuous indigenous habitation dating from the fifth century A . D . (Yapura phase pottery). The maloca, or communal roundhouse, has been a key organizational form for biosocial reproduction since prehistoric times. Oral history today includes references to constant wars with the Tukano peoples to the north and northwest of Yukuna territory as well as wars with the Witoto and Mirana peoples toward the southwest. During the Portuguese invasion in the sixteenth and seventeenth centuries, the indigenous populations were enslaved in the colonial plantations of Rio Negro. In the seventeenth century the Spanish colonizers forcibly relocated indigenous populations into mission villages, mingling enemy Indians in alien territories. As the colonists extracted spices, furs, and lumber, they imposed slavery and debt peonage on the Indians. According to present-day Yukuna, the most senior-ranking Yukuna were exterminated, and the juniors divided to form the present-day Senior and Junior ranks. During the rubber-boom era in the nineteenth century, the Colombian, Peruvian, and British dealers relocated and tortured the Yukuna, forcing some to migrate to rubber camps near the Colombo-Peruvian border area. There was an active Yukuna resistance, including armed and shamanistic retaliation against the rubber dealers and their armies. Yukuna coresidence with Andoke, Bora, Karihona, and Miranya Indians in the rubber camps of the Miriti area permitted a period of intercultural borrowing.
At the beginning of the twentieth century, the genocide and ethnocide perpetrated by the merchant companies that extracted rubber and gum decimated approximately 90 percent of these populations. The system of debt peonage in White-Indian relations prevailed in all the consecutive economic booms—the extraction of lumber, furs, fish, rubber, cocaine, and, most recently, gold. Nowadays, the majority of the Yukuna are living within resguardo territories, which are officially recognized by the Colombian government as communal Indian lands, and are governed by a cabildo of traditional authorities. In the 1980s the sporadic presence of heavily armed groups of non-Indians involved in illegal activities, as well as the invasion of the gold mines by thousands of Colombian placer miners, has aggravated interethnic tension in these territories. Recent migrations of Yukuna to the mestizo town of La Pedrera or to the city of Leticia, in search of wages and to escape retaliation from conflicts ensuing from the gold rush, have led to the polarization of the Yukuna into traditionalists and antitraditionalists.