top of page

Yellowstone Cutthroat Trout Management on the South Fork Snake River


  • Fall IDFG surveys estimated Rainbow Trout and Rainbow x Yellowstone Cutthroat Trout Hybrid abundances nearly doubled in 2018 and set a record high of 3,073 fish/mile in the Conant index reach.

  • If left unmanaged, Rainbow Trout would likely hybridize and out-compete native Yellowstone Cutthroat Trout in the South Fork Snake River.

  • To protect native Yellowstone Cutthroat Trout from a potential population crash and possible listing as a federal protected species, IDFG will electrofish Rainbow and Hybrid Trout during the 2019 spawning season and transport them to local lakes and ponds.

  • The South Fork Initiative recognizes this is not an ideal situation but we fully support the management decision to remove and reduce Rainbows and Hybrid Trout in order to protect native Yellowstone Cutthroat Trout.


Yellowstone Cutthroat Trout (YCT), Rainbow Trout, and Rainbow x Yellowstone Cutthroat hybrids (hereafter referred to as RHT – Rainbows & hybrids) all contribute to the world class South Fork Snake River fishery. Ideally, YCT and RHT could co-habitat with minimal inter-species competition and hybridization. Unfortunately, YCT and RHT share similar life-history strategies, utilize the same habitat, and compete for the same resources, with RHT exhibiting a competitive advantage in the system. RHT would likely hybridize and out-compete native YCT if left unmanaged in the South Fork Snake River. Since 2004, the Idaho Department of Fish and Game has been managing the South Fork Snake River to protect and promote YCT through a three-prong approach of excluding RHT from critical YCT spawning habitat, reducing RHT spawning success through a springtime freshet flow, and reducing abundance of adult RHT through angler harvest. The weir program has been effective at minimizing hybridization during YCT spawning at major tributaries but angler harvest and the spring freshet have been marginally effective at reducing RHT abundances. Recently, RHT abundances have increased exponentially in proportion to YCT abundances and pose a serious threat to the YCT population (Figure 1). To prevent the potential collapse of the YCT population, IDFG will electrofish RHT when they congregate at redds during the spawning season in 2019, remove them from the South Fork Snake River, and transport them to public lakes and ponds in the Upper Snake River region. The South Fork Initiative recognizes this is not an ideal situation but we fully support the management decision to remove and reduce RHT in order to protect the YCT population.

Figure 1. Rainbow and Hybrid Trout and Yellowstone Cutthroat Trout densities (fish per mile) at the Conant index reach of the South Fork Snake River, ID, 1982-2018.

Question and Answer

If you recognize that RHT and YCT both contribute to the world class South Fork Snake River fishery, why do you favor YCT?

RESPONSE: If the YCT population crashes there is potential they will get listed as a federally protected species through the Endangered Species Act, at which point management of the entire system would be hyper focused on YCT protection and recovery. This would likely mean aggressive RHT removal (electrofishing RHT off redds), prolonged recovery of a severely depleted YCT population (it is easier to protect a population of 1,800 fish/mile than recover a population of 200 fish/mile), and in the most extreme case, a shutdown of the entire fishery to prevent incidental by-catch and incidental mortality of YCT. While the most extreme case sounds unbelievable, a recent closure of steelhead fishing on the Main Salmon River and South Fork Clearwater River echo a similar situation. Even though hatchery steelhead are in the rivers and under normal circumstances could be caught and legally harvested, all steelhead fishing has been closed to prevent incidental by-catch and mortality of wild, ESA listed “threatened”, steelhead.

In summary, preventing a collapse of the South Fork Snake River YCT population is a better alternative than recovering a collapsed South Fork Snake River YCT population.

Okay, but what are the chances YCT get listed under the Endangered Species Act?

RESPONSE: From the 1880s through the 1980s, the introduction of non-native species (primarily Rainbow Trout, Brown Trout, Brook Trout, and Lake Trout), posed serious threats to pure, unaltered, YCT populations residing in their native range. In 1998, it was estimated that YCT occupied 43% of the historic range and only 17% of the populations exhibited no form of RHT introgression (May et al. 2003). Declining trends in YCT populations in their historic range motivated the petition to list YCT under the Endangered Species Act (ESA) in 1998. While the petition was officially deemed unwarranted in 2001, it emphasized the need to protect and prevent the decline of YCT populations to avoid future listing as a federally protected species.

From 1980-2001 (the period leading up to the ESA listing petition), YCT abundances averaged 2,541 fish/mile in the Conant index reach of the South Fork Snake River. Since 2002, YCT abundances have averaged 1,578 fish/mile. The recent increase in RHT abundances pose serious threat to YCT. If left unmanaged, the increased inter-species competition from RHT could severely impact juvenile YCT survival and overall YCT abundances in the near future.

I see the value in reducing RHT abundances, but what does this mean for fishing in 2019 and for the future?

RESPONSE: It is likely that your fishing experience in 2019 will be similar, or slightly less productive, than 2018. It largely depends on two things: 1) how effective IDFG electrofishing will be this spring and 2) whether you exclusively fish redds in the spring.

In spring 2018, IDFG performed a trial on select redds to see if there was a depletion of RHT abundances when removing RHT off the same redds for consecutive days. After several consecutive days of electrofishing the same redds, there was minimal depletion of RHT, meaning that as RHT were removed, just as many RHT replaced the fish that were removed the day prior. Obviously, this trend could not continue indefinitely, but this likely means that electrofishing redds could be a very effective approach for removing RHT.

On a positive fishing note (not a positive fishery note), trout abundances in the Conant survey reach were very good in 2018. Both RHT and YCT abundances increased in 2018, both were greater than their 10-year averages, and combined trout abundance set a record high of 6,253 fish/mile. Additionally, RHT abundances set a new record (3,073 fish/mile) and were nearly double their 10-year averages (1,615 fish/mile). Even if IDFG electrofishing was very effective at removing RHT this spring, IDFG has their work cut out for them to reduce RHT abundances to a level that would be noticeable by a seasoned South Fork Snake River angler who has been on the river for the last decade (IDFG would need to remove roughly half the current RHT population to reduce abundances to the 10-year average).

Removing RHT from the system will likely decrease total trout abundances in the short run, but it is expected that increases in YCT abundances will offset the decline in the long run. This hypothesis is founded in the data and the biology. YCT and RHT regularly occupy the same habitat and utilize the same resources. Removing RHT from the system will make more resources available to YCT and will promote increased YCT survival and recruitment. Additionally, 29 years of population data highlight that combined YCT and RHT abundances have remained fairly constant but the proportion of the total population has shifted towards RHT dominating the system (Table 1, bottom of blog).

Why did RHT abundances increase so much over the last two years?

RESPONSE: YCT and RHT recruitment have a positive relationship with spring and winter flows (Oldemeyer & Van Kirk 2018). Water years 2017 and 2018 had moderate winter flows and high spring flows and are the likely reason trout abundances increased in the South Fork Snake River. It is also possible that the increased spring flows made it difficult to target RHT in late spring and early summer, and angler harvest was lower than the 25-30% harvest of the annual population necessary to maintain or reduce RHT abundances.

What is a freshet flow and why didn’t it help reduce RHT?

RESPONSE: A freshet flow is a large flush of water that occurs during peak runoff. In unregulated systems, freshet flows are often large enough to move the river channel, mobilize substrate, and do significant morphological work on the floodplain. Native species that evolved in river systems with large freshet flows often developed life-history strategies that were adapted to the significant spring flows. For the native YCT, spawning later in the spring (May-July time frame) after peak flow and spawning in tributaries, were effective strategies to avoid having eggs dislodged from the substrate and getting swept downstream.

Non-native RHT have a similar life-history strategy to YCT with slight, but significant, differences. RHT typically spawn from February-May, and primarily spawn in the main river. In an unregulated South Fork Snake River system, spring freshet flows would likely be large enough to mobilize substrate and dislodge RHT eggs from their redds, making it difficult for RHT to recruit and reproduce naturally in the system.

One management strategy of the IDFG three-prong approach to reduce RHT abundances and protect YCT, was to work with the Bureau of Reclamation to increase flows after RHT spawning to mimic a freshet effect that would mobilize substrate and dislodge RHT eggs. Morphological and hydrological analysis estimated that flows needed to be on the order of 25,000+ cfs to mobilize substrate (Moller and Van Kirk 2003; Hauer et al. 2004). If 25,000+ cfs wasn’t achievable, increasing flows as high as possible, for as long as possible, was a secondary goal to try to achieve a freshet effect.

Since the implementation of the three prong-approach, the effectiveness of a freshet flow was never tested due to flood control constraints preventing flows from exceeding 25,000 cfs during post-RHT spawning period in the South Fork Snake River. Additionally, data now show that increasing flows in the spring actually had a positive effect on RHT recruitment (Oldemeyer and Van Kirk 2018).

In theory, increasing South Fork Snake River flows >25,000 cfs could still be an effective management strategy to mobilize substrate and dislodge RHT eggs. In practice, flows greater than >25,000 cfs aren’t realistic due to flood control constraints. It is likely that the system will no longer be managed to mimic a freshet effect because it isn’t feasible to release flows over 25,000 cfs and increasing flows during the spring that don’t exceed 25,000 cfs actually promote RHT recruitment.

What can I do to help?

RESPONSE: Plain and simple, harvest the RHT you catch. We know this is easier said than done. Many folks don’t want to deal with cleaning and cooking hundreds of fish, or getting your boat/cooler smelly when you have guests and clients on board. Additionally, we know it can be hard for many fly-fisherman, raised on catch-and-release principles, to give a rock-helmet to a beautiful 20” fish. If you can’t bring yourself to harvesting RHT, we would encourage you to support IDFG and other fisherman who do remove RHT, and help educate others that don’t understand why it is important to remove RHT in order to protect YCT in the South Fork Snake River.

What is IDFG going to do with all the RHT they remove?

RESPONSE: These fish are a public resource and IDFG will transport them to public ponds and lakes in the Upper Snake River Region that are NOT reconnected to the South Fork Snake River to promote other fishing opportunities.

Additional Information

If you have any additional questions or comments, please feel free to contact Bryce Oldemeyer at

Table 1. Point estimates for Yellowstone Cutthroat Trout (YCT), Rainbow Trout and Rainbow x Cutthroat hybrid trout (RHT), and total YCT + RHT per mile with respective 95% confidence intervals for the Conant index reach of the South Fork Snake River, ID, 1982-2018.


Hauer, F. R., M. S. Lorang, D. Whited, and P. Matson. 2004. Ecologically Based Systems Management: the Snake River - Palisades Dam to Henrys Fork. Final Report to U.S Bureau of Reclamation, Boise, Idaho.Flathead Lake Biological Station, Division of Biological Sciences, The University of Montana, Polson, Montana, 133 pp.

May, B., Urie, B., and B. Shepard. 2003. Range-Wide Status of Yellowstone Cutthroat Trout (Oncorhynchus clarki bouvieri): 2001. USDA Forest Service. Bozeman, MT.

Moller, S. and R. Van Kirk. 2003. Hydrologic alteration and its effect on trout recruitment in the South Fork Snake River. Report to Idaho Department of Fish and Game, Idaho Falls, ID. 92 pp.

Oldemeyer, B., and R. Van Kirk. 2018. Analysis of Relationships between Streamflow and Trout Populations on the South Fork Snake River. Project Report for the Idaho Department of Fish and Game. Boise, ID.

51 views0 comments


bottom of page