There has been no archaeological investigation of the Vaupés area. The first reports about this region are found in Pérez de Quesada (1536) and Von Hutten (1541), but systematic expeditions to the Río Negro were begun only toward the middle of the seventeenth century when the first mission villages and fortresses (S. José do Rio Negro, Taruma) were established. In the eighteenth century, in their aim to exert economic control over the area, both the Spanish and the Portuguese crowns sponsored expeditions and settlements to defend the border zones. At the end of that century and the beginning of the ninteenth, Luso-Brazilian expeditions reached as far as the Río Vaupés, promoting haciendas, animal farms, agricultural production, manufacturing, and handicrafts. Since the middle of the nineteenth century, centers of commerce have been encouraged. In reaction to abuse by missionaries and civilians, the Indians began to manifest their discontent and several messianic movements succeeded each other. From the end of the ninteenth to the middle of the twentieth century, the indigenous population was subjected to subhuman conditions as outsiders came to extract balata, chicle, and rubber.
Toward the middle of the twentieth century, the Colombian Amazon began to be invaded by colonists from the Andes; this was followed by the exploitation of cocaine and gold. The intervention of Protestant missions, the New Tribes Mission, and the Summer Institute of Linguistics was substantial, but their missionizing and catechizing have been rejected by the Cubeo. Part of Cubeo territory has been legally adjudicated to the Indians by the state, which is readjusting its health and education programs as well as other infrastructural enterprises. Because of Cubeo social and linguistic endogamy, trade with neighboring groups is probably recent. Some exchange is taking place with segments of the Guanano, Tukano, Desana, and other groups of the area. The Cubeo from the Río Querari, on the other hand, have tight links of economic, social, and cultural exchange with the Baniwa-Curripaco-Wakuenai, an Arawak-speaking indigenous group that has settled in the northern part of their territory. Their settlements on the riverine axis of the Vaupés, an important regional fluvial access route, has meant that the dominant society's exploitative and acculturative roles took a more dramatic form there than among other groups in the area. The strong tendency of the Cubeo to revindicate their sociocultural identity, however, offers resistance to miscegenation.