On the first Friday of each month, Brett High and his colleagues search through piles of frozen fish heads to see if any have coded wire tags affixed inside their snouts.

High, a regional fisheries manager with the Idaho Department of Fish and Game, explained anglers are essentially taking home a lottery ticket whenever they keep a rainbow trout caught from the South Fork of the Snake River.

Never before has the South Fork been as loaded with trout as it is now, according to Fish and Game population surveys. Unfortunately, it’s the invasive rainbows whose populations are booming, at the expense of the blue-ribbon fishery’s native Yellowstone cutthroats.

The department has placed a bounty on South Fork rainbows, giving anglers an incentive to keep more of them to thin their numbers. Fish and Game routinely captures rainbows, tags them and releases them back into the South Fork. Prize money ranging from $50 to $1,000 is awarded to any angler who turns in a head harboring one of the tiny, hidden tags.

Fish and Game started the Angler Incentive Program in 2010, following a year in which the South Fork’s rainbow population made a big jump.

“Harvest is one spot where we can really improve and do the most good,” High said. “The biggest threat to our cutthroat in the river are the rainbow trout, which can interbreed with and compete with the cutthroat.”

High said a few hundred fisherman participate in the program each year, many of whom regularly drop off bags of rainbow heads for the department to check, hoping luck is on their side. About 4 percent of the heads have tags, he said.

“Next week, we’re going to start tagging another batch,” High said.

Still, the program is falling short of its goals. Rainbow keep rates need to more than double to make a lasting impact on the fishery.

About half of the rainbows in the South Fork are caught in a given year, but only 15 to 20 percent of them are kept by anglers, High said. The department estimates at least 30 percent of the fishery’s rainbows need to be harvested to put a dent in the population. Anglers who catch more rainbows than they can eat may clean them and donate them to the department, which promptly delivers the fillets to local food banks.

The Angler Incentive Program, which operates on an approximately $7,000 annual budget, is one facet of a three-pronged approach toward boosting the South Fork’s cutthroat population. The department also seeks to give cutthroat an edge by releasing storage water to mimic the spring freshet, and by operating four weirs in key tributaries to prevent any trout without pure cutthroat blood from spawning.

In the 1980s, High said rainbow trout and brown trout were only present at low numbers in the South Fork. Annual monitoring showed rainbow trout and rainbow-cutthroat hybrids made significant gains throughout the 1990s, while pure cutthroats declined. At the low point in 2004, surveys showed the South Fork harbored 771 cutthroats per mile, compared with 2,400 cutthroats per mile in the 1980s.

“We’ve seen some rebound,” High said. “In last year’s survey, there were just over 1,800 cutthroats per mile.”

However, rainbows have fared even better, following consecutive wet years. Two years ago, the department’s survey showed the South Fork was home to 1,295 rainbows per mile. Last year, the population shot up to 3,073 rainbows per mile. The department’s ecological challenge represents the opportunity of a lifetime for anglers.

“For the first time on record, we’re over 6,000 fish per mile,” High said. “We’ll be looking as a department at really getting after those (rainbows) as best as we can. We may be manually removing fish and taking them to stock kids’ fishing ponds.”

To prevent hybridization, the department installed weirs in 2000 and 2001 across four key spawning tributaries — Burns, Pine, Rainey and Palisades creeks — allowing only cutthroat with at least 99 percent pure blood to pass. High explained department biologists use a visual test to identify pure specimens, checking for rainbow traits such as white tips on fins. Genetic testing has confirmed the visual inspections are remarkably accurate.

“Even though we have a lot of rainbows in the South Fork, we see low levels of introgression,” High said. “The percentage of rainbow trout alleles in cutthroat is about 25 percent.”

The third prong of the strategy involves coordinating with the federal Bureau of Reclamation on targeted spring releases of water from Palisades Reservoir. High explained cutthroat evolved with a spring freshet and get their cue to start spawning once the high flows drop. On average, High said there’s a sufficient water supply to support freshet flows once every three years.

The freshet also redistributes sediment, creating gravel bars where cottonwood seeds can take hold and sprout. Cottonwoods shade the water and provide habitat when branches fall into the river channel.

High said Fish and Game once believed simulating a spring freshet also served to wash away rainbow trout eggs and helped stymie their population while benefiting cutthroats. But evidence studied in recent years suggests a freshet of at least 25,000 cubic feet per second — a level that would flood homes and hasn’t occurred since 1997 — would be needed to curb rainbow reproduction.

Below that volume, High said ramping spring flows actually seems to benefit rainbows.

“From an ecological standpoint, the South Fork is the strongest population of river cutthroat in the state of Idaho. ... That’s unique. That’s something that has been lost from a lot of rivers in the West,” High said.