It is difficult to obtain information about the Apalai of the past because both archaeological data and historical documentation are lacking. Moreover, the few references dwell mainly on the location of villages. The oldest reports go back to the second quarter of the eighteenth century and state that the "Appirois" and Appareilles" inhabited the headwaters of the Jari and Oiapoque rivers. Following a period of silence, references from the second half of the nineteenth century reveal that Apalai communities occupied a vast territory, with concentrations on the lower courses of the Curuá de Alenquer, Maicuru, Paru de Leste, and Jari rivers. During this time, Apalai history can be traced together with that of the other indigenous groups of the Tumucumaque because they have many cultural traits in common, including the fact that most of them spoke Carib languages. They inhabited an area between the basins of the Trombetas and Jari rivers and their respective tributaries. Their almost complete isolation was only occasionally interrupted by hostile encounters with neighboring tribes, sporadic visits of travelers and scientists, and contacts mainly of a commercial nature with Guianese Maroons.
At the beginning of the twentieth century such contacts with the outside world increased, precipitating a drastic decimation of the indigenous population and promoting the regrouping and fusion of the survivors. Alarmed by these events, the Apalai initially retired to the headwaters of the Rio Maicuru and the lower and middle Paru de Leste and Jari rivers, including the latter's tributary, the Ipitinga. Finally, during the 1960s, they concentrated along the Paru de Leste. Their oral tradition recounts long periods of war, notably against the Cariban Wayana to the north and the Tupían Wayãpi to the east of their territory, as well as against certain hunting-gathering peoples whose survivors they incorporated into their own population. The process of fusion with the Wayana seems to have begun at the end of the nineteenth century, when the Apalai were concentrated on the Rio Paru de Este. According to mythical narratives, peaceful relations were established between these two groups when they allied themselves to destroy Tuluperê, a common enemy of supernatural origin.
There were Apalai contacts with nonindigenous populations (Brazilians and Guianese) at the beginning of the nineteenth century. Such contact has increased in the twentieth century and can be characterized as intermittent owing to the seasonal character of the region's extractive economy, which is based on balata, Brazil nuts, feline pelts (e.g., those of jaguars), gold, and tin; the Apalai used to participate in some of these activities and occasionally still do, either as extractors or providers of implements or foodstuffs to non-Indian extractors. In the 1960s the Apalai began to have permanent contacts with both missionaries and institutions of public service. The missionaries, who settled in the area in 1963, are evangelists representing the Summer Institute of Linguistics (SIL), a Protestant group, and the Baptist Alliance of the Amazon (ALBAMA). They devote themselves to the study of the Apalai language, which they use in their literacy work and in proselytizing, thereby exerting strong deculturative pressure. Government bodies are represented by the Brazilian Air Force (FAB) and the Fundação Nacional do Indio (National Indian Foundation, FUNAI). In 1969 the former installed a landing strip along the middle Rio Paru in a place known as "Apalai Village" and began a regular line of aerial transport. In 1973 FUNAI installed itself near the landing strip. At first this body's activities were of little effect; FUNAI limited itself to occasional hygenic assistance and the purchase of handicrafts. Later, the Indian post implemented more stable programs concerning hygiene and literacy in Portuguese. At the end of the 1980s, military control of the area was increased with the implementation of the CALHA Norte Project (PCN), and the Indian reserve of Tumucumaque became one of its areas of priority.