On a wet January night in northern California, Caleen Sisk-Franco gathered the Winnemem Wintu tribe for a healing in their prayer house, the sacred fire casting its walls with ocher shadow. Smoke from Ms. Sisk-Franco's pipe curled past her patient, a melancholy teenage boy from the neighboring Hoopa Valley Reservation.

As the tribe sang their song for lost little ones, Sisk-Franco, sensing the boy was nervous, took an eagle-feather fan from her doctoring chest and undulated it around his body. She then retreated into the shadows.

"There was the presence of your mom, trying to watch over you," Sisk-Franco said. "She's not around, but she wants you to know she cares about you.

"Where is your mom?" she asked. His teary gaze focused on the fire. "She died. A year ago."

Sisk-Franco is the spiritual leader and chief of the Winnemem Wintu, a small traditional native American tribe of 123 people, and she is also a well-known Indian doctor, or shaman. But one of Sisk-Franco's spiritual doctoring tools is technically illegal. This March, the US Fish and Wildlife Service revoked her right to possess eagle feathers because her tribe isn't recognized by federal authorities.

For thousands of years, the Win­ne­mem Wintu have practiced their culture among the sentinel pines and glacial waters of the McCloud River watershed, but that history is legally moot because they don't appear on the Bureau of Indian Affairs (BIA) list of recognized tribes.

So Sisk-Franco is no more eligible for an eagle-feather religious permit than a white Protestant, nor is her tribe eligible for other legal provisions meant to protect Indian cultures.

"We have to break the law in order to practice our religion and to be who we are," Sisk-Franco says. "They're basically saying, 'You don't know who you are. We know who you are, and you're not Indian.' "

The profiles of some federally recognized American Indian tribes have grown in recent decades as they parlayed their sovereign status to create profitable ventures such as gambling enterprises. But there are many other tribes that – never having had a reservation or simply falling through the cracks of Indian policy – are unrecognized by the United States. Scholars estimate that more than 250,000 of the 5 million who identify themselves as American Indians belong to about 300 unrecognized tribes, making them almost invisible to federal Indian law.

Unrecognized tribes like the Winnemem – one of several tribes that traditionally spoke the Wintu language – can't access the billions in federal benefits (as of 2005, the total was $4 billion), such as scholarships, Indian Health Services, housing grants, and other funding available to the 565 recognized tribes. Recognized tribes can also open casinos in some states and can more easily use federal laws to protect their religious ceremonies and land.

Many unrecognized tribes are no less indigenous than recognized ones: They practice living cultures, speak native languages, and some were previously acknowledged in some way by the US. The Winnemem, for in­stance, signed an unratified 1851 treaty and – in the 1941 federal act that created the 602-foot Shasta Dam – were identified as the tribe to be removed from the reservoir area.

These forms of acknowledgment alone don't constitute official recognition, which can only come from the BIA's Office of Federal Acknowledgment.

The OFA was created in 1978, with input from more than 300 tribal representatives, to standardize the recognition process and remedy a century of policies designed to assimilate or terminate tribes. That history complicates the OFA's task: How to fairly assess tribal identity when the US spent decades trying to undermine it?

How to define 'tribe'

To make these decisions, the OFA has four teams of anthropologists, genealogists, and historians who review tribal petitions – some of which are 100,000 pages long – and provide technical advice on how to complete those petitions. They make site visits, conduct interviews with tribal members, and spend an average of 25 months (including time for appeal) assessing a completed petition before making a decision, all in an effort to ensure that a limited pot of benefits is distributed fairly to historical tribes, says Lee Fleming, director of the OFA.

"The regulations allow for us to review any claim by any group from anywhere in the United States," Mr. Fleming says. "These claims must be supported by evidence to establish [the tribe] existed from historical times to the present and that the group does descend from Indian tribes."

While the Winnemem refuse to petition for recognition because they believe they should have been on the original list, Fleming says the process is necessary because of "instances where groups who have no Indian ancestry have forged documents and other records."

Some unrecognized tribes say the process has created a kind of caste system.

"We know our language and our history," says Daniel Romero Castro, general council chairman of the unrecognized Lipan Apache of Texas. "But we still fear the government is going to decimate us because they don't acknowledge our rights."

Qualified help from Obama

The divide between recognized and unrecognized tribes grew this December when President Obama endorsed the United Nations Declar­ation on the Rights of Indigenous Peoples, but excluded unrecognized tribes in the administration's position paper. Critics say it was an effort to reduce financial commitments.

"It's termination by accountant," says Bruce Granville-Miller, an anthropologist at the University of Brit­ish Columbia in Vancouver who studies unrecognized indigenous peoples around the world. "It's easy for nations to find ways to disqualify them, to make them simply disappear."

The OFA petition process is meant to help tribes gain recognition so they don't disappear. But many petitions languish for decades because of the costly process of documentation.

In the early 2000s, the Government Account­ability Office released several reports critical of the OFA's recognition process, finding it took excessive time to rule on completed applications (the BIA itself estimated in 2001 that it would take 15 years to clear its backlog), and that BIA decisions were often unclear. One case cited by the GAO involved a tribe granted recognition even though it had a 70-year gap in its documentation of continuous existence – a flaw that had doomed other petitions.

In response to the criticism, the BIA hired additional staff, developed a strategic plan, and posted a compilation of prior decisions that petitioning tribes could examine. GAO officials say timeliness and transparency has improved, but note there are still 265 groups that have submitted petitions the BIA deems incomplete.

Fleming says numerous tribes have found ways to complete the petition efficiently through grass-roots volunteerism and other efforts.

"They shouldn't hesitate to begin. Once they start the process they're able to receive technical assistance and advice from us," he says.

But some see that as the fox guarding the henhouse. For example, the Tolowa Nation, another northern California tribe, recently had its petition rejected after a 30-year effort because they didn't have enough evidence that they existed as a "distinct community" from 1903 to 1930.

"[The BIA] had a whole team of PhDs and anthropologists who seemed dedicated to undercutting our petition," says Martha Rice, a Tolowa council member. "For us, that's a tall mountain to climb."

Anthropologists and tribal members also argue that the requirement to show "continuous and distinct community" since 1900 is unrealistic given US history. "These people went through massacres, dislocations, and suffered all these horrible atrocities, and then the government demands, 'Show us your continuous community.' It's absurd," says Les Field, an anthropologist at the University of New Mexico in Albuquerque.

The BIA also solicits input on completed petitions from outsiders, which could include communities not wanting a nearby casino or recognized tribes who don't want their slice of the federal pie reduced, says Mr. Field.

But more than just benefits are at stake for unrecognized tribes like the Winnemem who say recognition would provide the basic legal protection their culture needs to survive.

Boaters versus sacred sites

That cultural battle is tangible on the banks of the McCloud River in northern California, where ancient Winnemem traditions take a beating by modern-day outdoor enthusiasts.

In the shadow of a traditional bark hut, a swirling filigree of bristly cedar, Sisk-Franco was teaching her 15-year-old daughter, Marine, to grind traditional medicines during a 2006 coming-of-age ceremony. The hut was erected on a traditional former tribal village site that the US Forest Service now runs as a public campground. But the Sisk-Francos' religious reverie was cracked when boaters motored past, their shouts – "Fat Indians!" "This is our river, too, dude!" – echoing across the canyon.

Despite the intrusion from boaters, the Forest Service denied the tribe's request for a four-day closure of 300 yards of river for their 2006 and 2010 ceremonies because the tribe isn't officially recognized. The agency provided a "voluntary closure," which several boaters ignored.

Fearing another ugly incident, the Winnemem postponed their 2011 coming-of-age ceremony for Marisa Sisk, the young woman training to be the next tribal leader.

"We've held these ceremonies for generations on the river, but our rights to [do it] aren't any more important than the boaters and fishermen," Sisk-Franco says.

The traditional Winnemem territory stretched 77 miles down the McCloud River to modern-day Redding. But they started losing land to ranchers and miners during the gold rush that began in 1849, and the construction of the Shasta Dam in the 1940s flooded more than 26 miles of the lower McCloud, including Winnemem villages.

The only tribal ceremonial sites the Winnemem can access are now owned by the government. The tribe managed to survive and carry on their traditions by holding ceremonies in secret and through the strength of Sisk-Franco's predecessor and mentor, Florence Jones, an internationally renowned Indian doctor.

Yet the Winnemem say their struggle is getting more challenging: The US Bureau of Reclamation is studying raising the Shasta Dam by six to 18 feet, which would submerge the coming-of-age ceremony site and most of what's left of the Winnemem's sacred places.

"Without our sacred places, without our ceremonies, we could no longer be Winnemem," Sisk-Franco says. "It seems like every time we have a bit of hope, it gets knocked down," she adds. "Then you wonder: How long can you keep that hope? And if you lose it, what happens then?"