An increase in brown trout helped boost the overall numbers.

Figures are closely watched by biologists trying to maintain a viable Yellowstone cutthroat trout population in one of the nation’s blue-ribbon fisheries.

In 1986, biologists counted a record 5,692 fish per mile in the South Fork, a stretch of the Snake in Idaho.

“Our estimates are pointing to good fishing to be had this year,” said Brett High, regional fisheries biologist for Idaho Department of Fish and Game.

Biologists have worked aggressively to attack the river’s exotic rainbow trout population, which breeds and competes with cutthroats.

Rainbow trout have increased from roughly 100 per mile in 1989 to 2,270 per mile in 2009, according to a 2011 report. Cutthroat trout peaked at 4,659 per mile in 1986 but fell to 771 per mile in 2004.

Since then, cutthroat have recovered and the rainbow trout growth rate has been slowed, High said. (See graph.)

“We recognize that there’s challenges that cutthroat trout continue to face in the South Fork,” High said.

On the upper Snake River in Jackson Hole, anglers occasionally see non-native trout — but they are rare. Fish counts are focused on cutthroat.

In the fall, biologists sampled a 5.5-mile section of the river between Moose and Wilson. They estimated 758 cutthroat per mile, up from 654 in 2008.

To keep rainbow trout in check on the South Fork, Idaho Game and Fish employs a three-pronged approach.

They use fish weirs to trap trout swimming into spawning streams and only let cutthroat reach spawning waters. Biologists ask Bureau of Reclamation officials to time releases from Palisades Dam to benefit spawning cutthroat, and they’ve encouraged anglers to kill and keep rainbow and hybridized cuttbows.

Rainbow trout are not native to the South Fork.

Each year, department workers catch several hundred rainbows and hybrids and insert tags in their heads. Anglers who return heads containing the tags can garner rewards ranging from $50 to $1,000.

Idaho officials are trying to protect cutthroat because they are an ecologically important native species and citizens value having the fish in the river, High said. Cutthroat are known for rising to dry flies.

Plus, states want to keep cutthroat, which were once prevalent throughout the West but now inhabit less than 15 percent of their former habitats, from coming under federal protection.

The fight against the rainbows is key to protecting cutthroats.

“The single-greatest factor in the decline of the cutthroat has been the introduction (both official and illegal) of non-native species such as the rainbow, brown, brook and lake trout,” A U.S. Fish and Wildlife Service paper on cutthroats states. “These exotic trout compete with cutthroats for food and habitat, and in the case of the rainbow trout, cross-breed with them to create genetically impure, but fertile hybrids.”

If the federal government were to step in to protect cutthroat in Idaho and Wyoming, management could be taken away  from the states, High said. The move could affect irrigators, anglers and outfitters.

In the fall, biologists counted South Fork fish by running electric current through the roughly two miles of river downstream from the Conant boat ramp in Swan Valley, Idaho.

The increasing fish counts can be ascribed to good water years as well as Idaho’s fish management practices, High said. Last year’s high water kept some anglers off the water and made fishing difficult when flows finally subsided.

On July 4, 2011, the river was flowing at more than 40,000 cubic feet per second, more than double the day’s average of 18,000 cubic feet per second, according to a BuRec website. In high water, fish move out of their normal holding areas, and murky water pouring out of tributaries makes angling difficult, High said.

“The fish definitely weren’t washed downstream,” High said.

During the fall fish count, the longest fish measured came in at 21 inches, High said. That doesn’t mean there aren’t bigger fish in the river.

Electrofishing affects only the top six to eight feet and not deep holes. Biologists, like many anglers, didn’t get to measure any of South Fork’s legendary trout.

“We don’t typically see them,” High said.

Taken from Jackson Hole News and Guide, author, Thomas Dewell.