When Stephanie Schmidt became Alaska’s Yukon River fishery research biologist in January 2012, she knew that all was not well along the sinuous length of the famed river. Chinook salmon numbers had been dwindling since 1998, and as a result, commercial harvest of the fish — also called king salmon for their immense size and sumptuous meat — was frequently halted. That didn’t help: The 2010 run was the second-worst in recorded history. 2011 was only a few fish better.

Faltering returns also hurt the Yukon’s subsistence fishermen, who catch chinook with nets and fish wheels to feed their families through the long Subarctic winter. But past hardships paled in comparison with 2014, their most difficult season yet. Earlier this spring, Schmidt and her colleagues at the Alaska Department of Fish and Game considered the dismal projections — an estimated 64,000 to 121,000 fish, pitiful compared to historic runs, which averaged 300,000 as recently as the mid-’90s. Then they made the painful decision to close the Yukon chinook fishery to everyone for the entire summer.

“I don’t want to say it was a no-brainer, because it was very difficult to know that people weren’t going to get the fish they depend on,” says Schmidt, a member of Wisconsin’s Brothertown Indian Nation who’s passionate about helping subsistence fishermen. “But when we crunched the numbers, it was clear: If we want to have any hope of meeting our objectives for escapement” — the number of fish that must survive to perpetuate the stock — “we couldn’t have any harvest.”

What makes the closure so frustrating is that researchers don’t know why the region’s chinook have vanished, or how to bring them back. In the Lower 48, such declines often have obvious causes: dams that impede migration, say, or the destruction of spawning grounds. On the relatively pristine and almost entirely undammed Yukon, though — and on other Alaskan rivers where chinook have nose-dived, like the Kuskokwim, south of the Yukon — the usual suspects don’t apply.

Less bycatch hasn’t produced more Yukon chinook — casting doubts about whether the pollock fishery was ever really the problem.

The king salmon’s disappearance is an ecological mystery as cryptic as it is alarming, and for the villages that dot the banks of the 2,200-mile-long Yukon — remote Alaskan and Canadian towns in which cash and employment are scarce and a gallon of gas can cost more than $6 — the salmon’s absence hasn’t just eroded fishing culture, it’s strained local health and prosperity. As one Alaskan put it: “I didn’t realize how much I depended on (the salmon) until I didn’t have it.”

Seven years ago, it seemed clear what was plaguing salmon: Alaskan pollock, the ubiquitous flakey white species featured in fish sandwiches at fast-food joints like McDonald’s. Although the Marine Stewardship Council considers the billion-dollar industry ––  America’s largest fishery –– sustainable, it’s impossible to haul 1.1 million metric tons of fish from the Bering Sea each year without landing a few others that you don’t mean to kill. In 2007, a decade into the salmon crisis, pollock boats scooped up a whopping 121,000 chinook as bycatch in their trawls; up to two-thirds would have returned to Western Alaska to spawn. Yukon salmon fishermen who had seen their own catches slashed were furious. “(The pollock trawlers’) difficulty is big, big money on one side, and small people on the other,” railed one Canadian fisherman.

To its credit, and with a hearty push from regulators at the North Pacific Fishery Management Council, the pollock industry responded with a suite of reforms. Many vessels voluntarily avoided bycatch hotspots and began using nets that allow strong-swimming chinook to escape while leaving weaker pollock ensnared. The industry developed incentives to reward the best performers and punish the worst offenders. And to ensure honest accounting, the fleet expanded the presence of fisheries observers, on-deck biologists funded by industry but managed by the federal government.

In subsequent seasons, bycatch indeed plummeted: Last year, pollock boats took just over 13,000 chinook. The fleet doesn’t necessarily deserve full credit for that reduction — fewer salmon in trawls might simply mean there are fewer salmon in the sea. Still, Stephanie Madsen, executive director of the At-Sea Processors Association, which represents a large portion of the pollock fishery, is sure the fleet’s actions have helped. “Nobody likes restrictions, but these guys can adapt,” Madsen says. “We’re confident that behavior’s changed, and we think those changes have resulted in lower bycatch.”

Less bycatch, however, hasn’t produced more Yukon chinook — casting doubts about whether the pollock fishery was ever really the problem. Salmon runs remain around 200,000 fish below historic levels, a discrepancy much greater than bycatch can explain. “The numbers just don’t add up,” says Daniel Schindler, a professor of aquatic and fisheries sciences at the University of Washington.

Still, down-and-out salmon fishermen continue to blame pollock. One group representing Native Alaskan villages threatened to boycott McDonald’s, and salmon stakeholders have repeatedly called for cuts to the pollock fishery’s allowable take of chinook. “Bycatch certainly isn’t the smoking gun,” says Diana Stram, a fishery analyst with the regional management council. But until chinook turn around in Western Alaska, it’s going to be a concern anytime one is caught as bycatch.”