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Resource polymorphism is a widespread phenomenon in post-glacial fishes where multiple morphotypes of a species occur sympatrically and exhibit distinct resource use. Availability of open niches and high levels of within and among species competition are thought to drive differences in morphology and may provide insights into early stages of speciation. Hovsgol grayling (Thymallus nigrescens) are endemic to Lake Hovsgol, a lake colonised by fish following the Pleistocene, and are threatened with habitat loss due to climate change and illegal harvest. Previous analysis of Hovsgol grayling diet inferred through C and N stable isotopes suggested the presence of littoral and pelagic foraging groups. We hypothesised that morphology of the two foraging groups would reflect predictions of functional morphology, indicating the presence of resource polymorphism. To test this hypothesis, we evaluated evidence from C and N stable isotopes, stomach contents, fish ages, capture location and morphology. Two foraging groups of Hovsgol grayling were identified through stomach content and C and N stable isotope analysis. Individuals with greater zooplankton consumption were more frequently captured in the pelagic zone, exhibited higher gill raker counts, larger orbit (eye) sizes, longer paired fins, narrower head width, larger maxilla and smaller size at age than the group with greater reliance on benthic invertebrate prey. These differences were generally consistent with those described in other fish species exhibiting littoral-pelagic resource polymorphism. Our study provides the first example of littoral-pelagic resource polymorphism in the salmonid subfamily Thymallinae and highlights the potential influence of competition on fish evolution.