The one issue that has loomed over all others during the initial stages of the project is the native Yellowstone cutthroat versus rainbow trout dilemma. It is a dilemma because both fish are naturally reproducing (i.e., wild) in the system, and anglers in recent years have become attached to the aerial displays and fighting vigor of both the rainbows and hybrids in the South Fork. Unfortunately, from an ecological perspective, the rainbows are extraordinarily detrimental to the system because they interbreed with the native fish thereby diluting the genetic integrity and threatening the long-term persistence of the cutthroat.
Because of the historic stocking of rainbow trout in the South Fork Snake River watershed, the fish gained a toe-hold in the system sometime in the early 1970s. It is interesting to note that despite the fact that the fish were sporadically stocked at various times and locations for most of the past century in the South Fork watershed, they were not documented or considered part of the wild fish assemblage in the wildest canyon section of the river until IDFG electro-fishing surveys counted sixteen rainbows in the Conant Reach (estimated at the time to translate to less than one percent of the fish population for that reach of stream) in 1982.
Since 1982, the percentage of rainbow and hybrid trout in the Conant reach has increased at an alarming rate. As with most complex biological and ecological issues, there are a number of factors that may have precipitated - or most likely combined to precipitate - the rainbow increase. The bottom line - whatever the multitude of causes - is that the rainbow populations have really taken hold. IDFG surveys of the Conant reach in 1995 found 430 rainbows and hybrids per mile constituting 16% of the fish population. In 1996, this number rose to 972 fish per mile in that river reach (27% of the fish population). Finally, IDFG surveys in fall 2002 registered 1,300 rainbows compared to about 1,350 cutthroat (34% of the fish population); this was the first year that rainbows essentially equaled cutthroat numbers in this part of the reach.
In recent months, the Idaho TU Office and local TU chapter (Snake River Cutthroats) have worked very closely with IDFG regarding possible solutions. Obviously, we will all continue to work on research and advocacy issues related to water management and other issues that will in the long-term provide spawning and recruitment benefits for native cutthroat trout. Further, IDFG is planning on continuing the operation and maintenance of the tributary weirs to ensure that the South Fork's primary spawning tributaries - Burns, Pine, Rainey, and Palisades creeks - remain refuge areas for the river's native fish. But this is a costly and time-intensive approach that merely treats the symptoms and not the problem regarding introgression in the South Fork watershed.
In the short-term, however, TU and the agency agree that encouraging angler harvest of rainbows is the most time- and cost-effective manner to keep the rainbow population in check. It is important to note that this is not a wild trout eradication effort. It is a native trout conservation effort that includes a harvest component so that the rainbow population is restored to a manageable level - somewhere between 5-15 percent of the overall fish population. During the winter, TU and IDFG initiated a couple of introductory outreach meetings first with, the local fly fishing community and later with the core group of South Fork outfitters. Based on these meetings, one thing is clear: both anglers and the businesses that depend on the South Fork fishery are concerned about the long-term persistence of the South Fork's native cutthroat.