The video, taken from a motorboat near Peru’s Manú National Park, shows five naked men walking along a riverbank. As the boat approaches, one man brandishes a bow. “Arrow! Arrow!” warns a voice in the boat.

That footage of members of an isolated group of indigenous people was released by Peru’s Environment Ministry in October, shortly after an indigenous park guard at Manú was shot in the back with an untipped arrow—not meant to kill, but a clear signal that he was getting too close. Both events came barely a year after a film crew captured footage of adults and children, their bodies painted red and black, near a thatch-roofed dwelling in a remote region of western Brazil, not far from the border with Peru.

Less than a century ago, indigenous people fled to distant corners of the Amazon rainforest to escape enslavement and death at the hands of rubber barons and to live in what is known as “voluntary isolation.” Today, their descendants still shun contact with the outside world, but they are being squeezed as their once-safe areas become more accessible to tourists, scientists, oil-drilling crews, loggers and drug traffickers.

This not only has put the once-unmolested indigenous communities at risk, but also the strikingly healthy ecosystem they inhabit—typically mature, intact, biologically diverse forests that would merit conservation purely on environmental grounds.

“Isolated peoples live in the healthiest forests,” where game has never been frightened away by armed hunters, says Carlos Soria, the secretary general of Peru’s National Protected Areas Service (Sernanp).

Just west of Manú, the crown jewel of Peru’s park system, is the Nahua-Kugapakori-Nanti Reserve, which was designed to protect Nahua and Nanti indigenous people living there in isolation. The reserve borders Manú, essentially extending the park and biosphere reserve, but the protection is not absolute.

One well of the Camisea gas field, Peru’s largest current source of natural gas, lies within the Nahua-Kugapakori-Nanti Reserve, and the consortium operating the field, which is led by the Argentine company PlusPetrol, would like to drill another.

Under Peruvian law, such reserves are considered “untouchable,” unless exploitation of them is judged to be in the “national interest.” That exception, says anthropologist Richard Chase Smith, director of the Institute for the Common Good, which helps indigenous communities defend their territorial rights, “makes the whole law kind of laughable.”

In October, a Peruvian government official lost her job after she questioned an environmental and social impact statement for expansion of the Camisea operation into the Nahua-Kugapakori-Nanti Reserve.

Raquel Yrigoyen, who was named by the new government of President Ollanta Humala in September to head Peru’s National Institute for Development of Andean, Amazonian and Afro-Peruvian Peoples (Indepa), said a lower-level Indepa manager in the previous administration had signed off on the study without the required approval from top Culture Ministry officials.

She was removed from her post on Oct. 19, after issuing a resolution nullifying that approval and calling for a new review of the study based on scientific criteria and international standards for protection of isolated indigenous peoples. Yrigoyen, who now heads the nonprofit International Institute on Law and Society (IIDS) in Lima, says members of Congress also had complained to her office of illegal incursions in the reserve. She says people had reportedly been entering the reserve to carry out studies without the required authorization from local indigenous communities that are in contact with the outside world.

In Peru, 2.8 million hectares (6.9 million acres) of land, mainly near Manú and the Brazilian border, are set aside in five reserves for isolated indigenous groups. Five more such reserves have been awaiting approval. Protection serves two purposes: it keeps ecosystems intact, enabling the inhabitants to survive there; and it reduces the risk of exposure to diseases, including common ones such as flu, to which they have no resistance.

There is virtually no control over access to the areas, however, and indigenous leaders, human rights activists and environmentalists have complained about illegal logging and incursions by drug traffickers, as well as overlapping oil and gas leases.

One proposed reserve is on Peru’s northern border with Ecuador, not far from Ecuador’s Yasuní National Park, which is considered one of the hottest of the world’s biodiversity “hotspots” because of the enormous variety of species that have been found in a small area. Yasuní’s biological riches sustain two groups of semi-nomadic people, the Tagaeri and Taromenane. The two groups opted for isolation even after groups of Waorani, to whom they are related, accepted contact from missionaries in the 1950s and began to settle in villages.

Yasuní sits atop an oil deposit containing an estimated 900 million barrels, which the government had planned to open for drilling. In response to an international campaign opposing the plan, because it threatened both the megadiverse ecosystems and the people living there, President Rafael Correa offered to leave the oil in the ground if industrialized countries provided $3.6 billion in compensation, about half the estimated value of the oil.

This month, Ecuadorian officials said they had met a deadline for raising $100 million by the end of 2011 for the compensation fund, which is being managed by the United Nations Development Program. But some observers questioned whether the milestone was truly reached. They pointed out that half the amount was a debt swap with Italy and much of the rest had not yet been deposited in the compensation fund. Still, supporters note that the novel approach has helped put Yasuní—and the nexus of conservation and isolated peoples—on the map.

In lesser-known places facing similar problems, the battle is more difficult. The word “biodiversity” typically conjures images of rainforest habitat such as that of Yasuní or the Peruvian-Brazilian border, where most of the world’s isolated indigenous people are located. But scientists say it also applies to another area where these people live: the semi-arid Chaco region of northern Paraguay. From the wetter east to the drier west, different rainfall levels and soil types give the Chaco a variety of ecosystems, ranging from savannah and open woodland to dense, tangled thorn forest, and a rich diversity of plant and animal species.

That diversity once sustained the Ayorea people, who originally ranged over an area the size of Italy, according to Benno Glauser, who works with the Amotocodie Initiative, a nonprofit in Filadelfia, Paraguay, that advocates for indigenous rights. Some of their descendants still live in isolation in increasingly fragmented forests in both the western and eastern Chaco.

About one million hectares (2.47 million acres) are in government-designated natural protected areas. Although they provide some protection for the isolated people, they were designed with environmental criteria in mind and “do not [necessarily] coincide with the territory used by the isolated people,” says Glauser, who calls for a more “holistic” approach to the planning of protected areas.

Much of the land in the Chaco is in private hands, and the remaining forest is under pressure from ranching, oil and gas exploration, land speculation, drug traffickers who clear clandestine landing strips and private conservation areas for carbon credits, whose managers do not want indigenous people using resources on their lands, Glauser says.

He disputes the belief that isolated groups will automatically migrate to protected areas, where they will be safer. “Isolated peoples live where they want to,” he says. “Sometimes that coincides with park land and sometimes it doesn’t. It’s necessary to identify those territories, demarcate them and then grant titles in the name of those groups.”

That is the approach taken by Brazil, where the government office charged with looking out for isolated people’s interests has set aside large swaths of forest for them.

Brazil is the only country in their region with an office dedicated to protecting the rights of isolated people and those who have taken the first steps toward contact with the outside world. In the 1900s, Brazil’s policy was to contact isolated groups and relocate them, in an effort to protect them from advancing loggers and ranchers.

Strategy shift

But the policy took a dramatic turn a few decades ago, and the practice now is to define the boundaries of the areas used by isolated tribes and put them off limits to outsiders.

Those reserves are “a recognition of the inalienable and inexorable link between indigenous people and the land they live on,” says U.S. journalist Scott Wallace, who accompanied Brazilian government officials on a 2002 expedition to determine the boundaries of territory used by an unidentified group known only as the Flecheiros—the “People of the Arrow.”

“These are small groups perched on land with lots of resources, but the fact of the matter is that these are the original inhabitants of these areas. They are really the rightful owners,” says Wallace, whose book about the expedition, “The Unconquered: In Search of the Amazon’s Last Uncontacted Tribes,” was published in October.

Brazil has 23 isolated groups, according to the National Indian Foundation (Funai), the government indigenous affairs agency. Most are near Brazil’s western and northwestern border. Once a group is located, Funai tries to establish the boundaries of its territory, demarcate the area and set up controls to keep other people out. The result is a de facto extension of the country’s natural protected areas.

But the system is not fail-safe. In July, a group of about 40 armed men believed to be drug traffickers traveling east from Peru overran a guard post that had been set up near the Peruvian border to control entry into a reserve for an isolated group. And Wallace reports a case in which indigenous people living outside a reserve lured an isolated family to their village with gifts of salt and other items.

Not all of Brazil’s isolated indigenous people live in large expanses of forests near the country’s borders. Some live in forest fragments in the interior of the country, surrounded by encroaching ranches and cropland.

Added pressure

Those areas are under even more pressure, according to Antenor Vaz, who heads Funai’s Isolated Peoples Department, because of agricultural runoff and other pollution from farms and ranches upstream. Nevertheless, the people inhabiting them help protect forest that might otherwise be cleared for agriculture.

Although indigenous-rights activists and environmentalists might seem to be natural allies in the battle to safeguard sensitive ecosystems, there is a long history of tension between these groups in Latin America. Environmentalists have often pushed to keep protected areas free of human habitation, causing indigenous leaders to accuse them of caring more about animals than people.

But the people-or-conservation dichotomy is false, says geographer Susanna Hecht of the University of California at Los Angeles, who has studied the history of human habitation near the Peruvian-Brazilian border.

“There’s a really big human footprint in Amazonia,” Hecht says, citing research indicating that indigenous inhabitants of the Amazon historically have done more intensive forest management than was previously believed.

For Wallace, the connection between environmental conservation and protection of isolated people’s territories became clear during the three-month expedition, navigating upriver and hacking through the dark, claustrophobic understory in the Javarí watershed.

For isolated indigenous people, “their livelihood, their mythology, their beliefs, their universe is linked to the land upon which they live,” Wallace says. “This is both a human rights issue and an environmental-conservation issue. You can only protect uncontacted groups by protecting the forests they live in and letting them live as they have for millennia.”