The Eurasian Triturus karelinii group of crested newts comprises three distinct, geographically coherent mitochondrial DNA lineages, designated as the eastern, central and western lineage. These three lineages are genetically as diverged as other, morphologically well-differentiated crested newt species. However, on the ground of restricted morphological studies the three lineages have been considered morphologically uniform. We analyze skull shape in the T. karelinii group using geometric morphometric techniques and interpret the results in a phylogenetic context. We found a high divergence between populations and variable patterns of sexual dimorphism within mitochondrial DNA lineages, significant divergence in skull shape including significant divergence in allometry of the ventral skull side in females, and lack of concordance between the pattern of morphological and genetic variation within lineages and between lineages. The observed pattern indicates that ecologically mediated divergences could play an important role in the evolution of skull shape. Reconstruction of the evolutionary trajectory of the T. karelinii group indicates that the eastern lineage largely retains the ancestral skull shape and that the central and western lineages possess a derived skull shape. Skull shape does not clearly support the presence of three discrete geographical groups as suggested by the mitochondrial DNA data, but the amount of shape changes between T. karelinii lineages is similar to that between T. karelinii lineages and the outgroup species, T. macedonicus.