The genus Brachymystax is represented by three putative species that disjointedly inhabit the major river basins of central and northeast Eurasia. Brachymystax lenok and B. tumensis have been regularly misidentified throughout their range, including across sympatric populations in the upper Onon River of Mongolia. This research has focused on Mongolia’s understudied lenok populations by conducting detailed morphometric measurements and genetic analyses to confirm key metrics for accurately distinguishing between these cryptic species. While there are slight differences in colouration and patterns including size and density of their defining black spots, four key metrics were found to be significantly different between the species including gill rakers counts, snout length, lateral line scale counts and body depth. Brachymystax tumensis was also typically heavier than B. lenok at the same length. These results were supported by genetic analyses which clustered the two species into separate clades and displayed unique haplotypes for the Mongolian populations. Initial investigations of diets and gonad maturation indicated an ecological and spatial separation of these sympatric species. The current study is important for these recreationally targeted species which require further research and species-specific management measures to ensure their threatened populations are conserved in Mongolia for the future.