A fish long thought to be extinct has been rediscovered in southwest Colorado as government biologists use genetics to unscramble which species belong and which don’t after 150 years of human meddling with life in mountain streams.

Yet within a few months of confirming the remnant group of San Juan cutthroat trout — transplanted on a hunch in 1989 for safekeeping in isolated Hermosa Creek headwaters, then verified this year against a 144-year-old sample at the Smithsonian — a raging wildfire north of Durango threatened their survival.

As flames from the 54,129-acre 416 Fire spread toward the stashed cutthroats this summer, a Colorado Parks and Wildlife team — including a biologist who devoted three decades to identifying them as a unique subspecies — hiked to those headwaters and rescued 30 of the trout. The CPW team trekked back, again, after flames scorched the area, and rescued 28 more before rainfall triggered debris flows that can be deadly for fish.

State biologists now are holding the 58 rescued San Juan cutthroats in hatchery quarantine tanks. They plan to breed the fish to enable an ecological rescue. It’s the latest of multiple Colorado efforts to rescue lost species and re-engineer altered habitat for survival of genetically robust native species.

“It has always been the Holy Grail to go back to how it was before European settlers,” CPW aquatic biologist Jim White said in an interview Wednesday. “Preserving native diversity across the landscape is part of conserving that landscape. People often want to know we’re taking care of our environment. These fish are a symbol of that. And people like to know that there are still wild places.”

The survival of the San Juan cutthroat in the wild — as with the greenback cutthroat rediscovered on the southeastern side of Pikes Peak near Colorado Springs — depends on whether the fish can handle changed conditions. They evolved in cold, high lakes and headwaters. Water diversions, dams and climate change increasingly reduce stream flows, while non-native fish competitors stocked in streams for more than a century starting as a food source for miners, pollution and degraded stream banks all present obstacles.

Colorado biologists said this week they hope to reintroduce offspring of their 58 rescued San Juan cutthroats next year in a stretch of Wolf Creek that the U.S. Forest Service is helping to revitalize.

State analysis of an 1874 specimen of the San Juan cutthroat in the Smithsonian National Museum of Natural History, compared with DNA samples snipped from suspected survivors in Colorado, verified this year that this type of fish has not vanished as once thought.

This ecological rescue could succeed if habitat can be found, said David Nickum, director of the conservation group Colorado Trout Unlimited.

“Fortunately, southwest Colorado — despite many challenges from abandoned mines — still has extensive, highly protected habitats in some of the state’s largest wilderness areas,” he sad. “We’re hopeful that several suitable locations can be found as new homes for these unique fish, enabling them to return to their home range and provide a solid basis for long-term protection.”

Cutthroat trout originated in the Pacific Ocean. Biologists have identified 14 subspecies, including three types surviving in Colorado. Those are the Colorado River cutthroat found west of the Continental Divide, the Greenback cutthroat in the South Platte River Basin and the Rio Grande cutthroat in the San Luis Valley.

A fourth subspecies, the yellowfin cutthroat native to Arkansas River headwaters that weighed up to 10 pounds, disappeared in the early 1900s, according to the latest fish extinction research.

The cutthroats from each area have distinctive genetic markers.

Colorado aquatic biologists currently are propagating the three types confirmed here. They’re treating the San Juan cutthroat as a lineage within the Colorado River cutthroat subspecies for now, with the aim of reintroducing them statewide.

This rescue began in the 1970s, when state biologist Mike Japhet had a hunch. For 15 years, he and colleagues hunted for fish in isolated high, cold waters above waterfalls that they suspected might hold remnant populations of native cutthroats. They relied on painstaking investigation of physical characteristics to distinguish different fish, including the examination of scales, spots and teeth at the back of the tongue. They finally found likely candidates in 1989.

The biologists deployed a helicopter for a transplant operation at an elevation around 9,500 feet using the most secure and isolated headwaters they could find — along tributaries of Hermosa Creek north of Durango.

“We took out probably 150 fish,” Japhet recalled Wednesday. “We electro-fished and captured them and packed them to a clearing where a helicopter could hover overhead, loaded the fish in plastic bags with oxygen and ice and water, and put in a cargo net. The helicopter lifted them up, flew a few miles, and lowered them back to the ground where we had another crew waiting.”

DNA analysis wasn’t yet possible. “We had no idea,” he said.

In 2012, Colorado biologists and a University of Colorado researcher teamed up to investigate another cutthroat presumed extinct — the Greenback — had survived. They went to the Smithsonian Museum.

While Greenback testing proved conclusive, the initial analysis of two preserved samples of the San Juan cutthroat collected in 1874 near Pagosa Springs by naturalist Charles Aiken failed to verify the status of the San Juan cutthroats in Colorado. It wasn’t until last winter, after CPW crews and genetics researcher Kevin Rogers had collected DNA samples on the Hermosa headwaters transplants, that biologists concluded they survived as a unique type of fish.

“We had this original diversity of cutthroat trout across the landscape. We have lost the vast majority of it since European settlement,” Rogers said. “We’ve lost so much. But there are still some pieces of our heritage out there.”

Modern DNA analysis increasingly “lets us parse out quickly who belongs where. It is a much easier test than trying to take individual fish and compare them as taxonomists of years past would have done.”

Japhet, 67, retired in 2008. But now he’s back on the job, temporarily. His hunt for the San Juan cutthroat “was a career-long quest,” he said.

“This feels great. For a retired person, it makes you feel like your life’s work was worth something.”

The hunch he relied on through the 1970s was rooted in guiding principles inspired by ecologist Aldo Leopold “that there are a lot of benefits of preserving native species, to preserving all the parts — just to leave a part of the natural world intact for our successors so they can have some inkling of what it was like here before man changed the whole ecosystem.”