Not long before the European Conquest, Guaraní raids were being conducted into what is now eastern Bolivia for the purpose of capturing women and slaves. In particular, groups of warriors from the Río Itatin region were making frequent forays into southern Bolivia. They gradually defeated local peoples like the Chane, whose land they occupied and whose people they enslaved. Eventually, these new arrivals became known locally as the "Chiriguanos." With the arrival of the Spanish from Asunción, Paraguay, in the late 1500s, the Chiriguanos unsuccessfully waged war on these new intruders. Once defeated, Chiriguano survivors were relocated at mission outposts ( reducciones ) established by Jesuit and Franciscan friars. It is probable, however, that several bands of Chiriguano escaped detection by fleeing into remote areas of heavy forest, where they were able to live in relative isolation.
The Yuqui are very likely a remnant population of these people. Even today, they are culturally and linguistically similar to many northern Paraguayan groups such as the Ache, giving credence to their recent shared origins. Their cultural as well as biological proximity to the Siriono is attested by the unusual congenital ear notches that are evident among both groups. Generations of living as fugitives and infrequent encounters with a growing mestizo population, which resulted in the spread of disease or outright killing, gradually took their toll on the Yuqui, reducing their numbers significantly. This process would also account for the degree of deculturation that has occurred among the Yuqui.
In spite of earlier suppositions that the Yuqui as well as their Siriono cohorts represented the simplest form of adaptation to the lowland South American environment, further study points to a loss of culture content as a more likely explanation for the lack of cultural complexity among both groups. Vestiges of Yuqui deculturation from a more complex level of cultural organization include leadership rights that are inherited through the male line, the existence of hereditary slavery reminiscent of a slave class or caste, and the presence in the Yuqui language of common Tupí-Guaraní words for cultivated crops (maize, ibachi; manioc, ndio ).
Relations with all outsiders (Aba) were traditionally hostile. Whites or mestizos were thought to be the spirits of dead Yuqui and were greatly feared. The word "Aba" probably derives from a term used by Guaraní invaders, whom the Yuqui consider to be their own progenitors (there are still Guaraní people known as "Ava"). Nevertheless, because these outsiders, or Aba, are not known Yuqui and therefore must be spirits of dead ancestors, they are regarded as enemies to be destroyed. This reaction is consistent with the belief held by the Yuqui until peaceful contact occurred that they were the only living beings on earth. In the mid-1950s increasing hostilities with settlers moving into Yuqui territory resulted in the arrival of missionary contact teams organized by the New Tribes Mission, a group of North American Protestant fundamentalists. Following more than ten years' of cutting gift trails, leaving gifts for the Yuqui along these trails, and gradually establishing peaceful relationships with a band of fortythree individuals, the mission convinced the group to give up its nomadic existence and hostilities with the outside world. They were settled at a camp on the Río Chimore. In late 1986 and 1989, what were probably the last two remaining bands of forest Yuqui were successfully contacted and encouraged to relocate to the Chimore camp. With natural increase and the addition of the two new bands, both closely related to the original band contacted, the population had reached 130 by 1990.