The icy waters of Slough Creek in Yellowstone National Park meander through a spacious valley, beyond open meadows, where the craggy summit of the Beartooth Mountains rises to 9,000 feet. Craig Matthews, an ardent conservationist and the owner of Blue Ribbon Flies, wades in up to his waist. He ties a small dry fly onto his rod and casts, moving his rod back and forth like an eight-foot metronome. The fly lands gracefully at the head of a pool and moments later a large Yellowstone cutthroat sucks it down. Matthews expertly plays the fish and nets it. The 21-inch cutthroat’s crimson slash, golden hue, and black spots seem more likely to have been adorned by an artist’s brush, rather than the result of millions of years of evolution. 

The Yellowstone cutthroat is one of approximately 12 subspecies of native cutthroat trout found in clean, cold streams and lakes in North America. Each species is identified with its own geographical region and distinct markings. The 90,000 acres of Yellowstone Lake are the last stronghold of the species.

Yellowstone cutthroats dine primarily on insects, but will occasionally pursue juvenile sculpins, whitefish, suckers and even small trout. They sip delicate mayflies hatching on the water’s surface, hunt stonefly nymphs clinging to smooth river cobbles, and even consume grasshoppers that fall into the water.

But they’re more widely-known for their role as prey, not predator. Cutthroats support a $36-million sport-fishing industry in the park and surrounding communities, and they provide an essential source of food for many animals. “The cutthroat is an important link in the food chain of the park—from invertebrates to higher level consumers [like grizzly bears],” says Todd Koel, supervisory fisheries biologist at Yellowstone National Park.

In the spring, grizzlies emerge from hibernation and fatten themselves on cutthroats spawning in the tributaries of Yellowstone Lake. Bald eagles and ospreys snatch wriggling cutthroats from the lake shallows and feed them to their young. Otters chase trout through mazes of submerged tree branches.  “The cutthroat lies at the heart of the Yellowstone system,” says Koel. Indeed, other fish, like the introduced lake trout, can’t replace cutthroats in the food chain because they generally swim 50 to 100 feet below the surface, well beyond the reach of birds, grizzlies, and otters.

That’s why the cutthroat’s dwindling numbers are cause for concern. In 1999, a fish census recorded more than 2,300 cutthroats in Bridge Creek, a tributary on the west side of Yellowstone Lake. But five years later, only one cutthroat was counted there. It was a similar story at Clear Creek, on the lake’s east side, where 1,438 cutthroat were counted in 2004, down 58 percent from the previous year.

So what accounts for the diminished cutthroat numbers in Yellowstone? One answer is the predatory lake trout, which was first discovered in 1994. No one is exactly sure how the lake trout were introduced, though many suspect they were covertly introduced by an angler. Today, the lake trout problem boils down to simple arithmetic: These large, voracious fish can consume up to 42 cutthroats per year. To cull the lake trout, Todd Koel’s fisheries team gill nets them in Yellowstone Lake from May through September. Since the mid-1990s, they’ve netted nearly 200,000 lake trout. But Koel admits, “The lake trout have a free run of Yellowstone Lake seven months of the year,” when the surface is frozen over.

Lake trout aren’t solely responsible for the cutthroat’s decline. Whirling disease, a parasitic protozoan from Europe, kills young cutthroats in streams. The microscopic organism is believed to have been introduced to North America though contaminated fish parts from Denmark, which somehow entered wild streams. Whirling disease can move downstream at an astonishing rate of 15 to 20 miles a year, and neither cutthroat nor rainbow trout are immune. 

Every summer, drenching rains increase stream flows and allow young cutthroats to migrate back to Yellowstone Lake. But recent drought conditions have led many tributaries to dry out, isolating the young cutthroats in small pools. These recently hatched fish quickly become easy pickings for gulls, pelicans, and other predators.

Hybridization is yet another threat to Yellowstone cutthroats. When cutthroats live in the same water as rainbow trout, they often produce offspring together, resulting in handsomely colored fish. But fisheries biologists contend that the “beauty is only skin deep” and worry that hybridization will inevitably bring an end to the cutthroat’s genetic purity, altering its role in the ecosystem.

Though the cutthroat’s numbers have been drastically reduced, the U.S. Fish and Wildlife Service concluded in 2006 that it does not warrant endangered species protection. Moreover, not all stakeholders agree on whether an endangered species listing is desirable.

Koel maintains that halting the spread of exotic species such as lake trout and whirling disease is critical to saving the Yellowstone cutthroat. He also urges anglers who catch cutthroat to release them and take home introduced fish like rainbow trout instead. Finally, Koel believes that one of the best ways to preserve the Yellowstone cutthroat is to encourage a broad spectrum of people to fish in Yellowstone: “The more we put native fish in the hands of kids and people in the city,” he says, “the better off species like the cutthroat will be.”