Siberian taimen Hucho taimen (Pallas, 1773) is a broadly distributed and popular sport fish with high economic value. However, low abundance and hard-to-reach habitat make the Siberian taimen a relatively understudied species. Here we describe the morphological variability of two size groups of Siberian taimen juveniles from the eastern (Amur River basin) and western (Kama River basin) parts of the species distribution. The largest morphological differentiation of Siberian taimen juveniles was observed at the inter-basin level. In the Amur River basin, Siberian taimen juveniles also differed morphologically even at sites located at a distance of 20 km from each other, which may be explained by a small home-range inhabitation of juveniles leading to the formation of their morphotype determined by local environmental conditions. The pattern of allometry varies in taimen from different rivers, which could be related to the ontogenetic shift of ecological niches and the level of heterogeneity of the river environment.