European mustelids include the European polecat, Mustela putorius, and the steppe polecat, M. eversmanii. Both occur sympatrically in the Pannonian Basin, where M. eversmanii hungarica represents the westernmost part of the latter species and they allegedly hybridize. We investigated the morphological relationships in sympatric and allopatric populations of these mustelids with representative sampling, taxonomic and geographic coverage. We evaluated inter- and intraspecific patterns of morphological differentiation of 20 cranial measurements and four external traits by distance-based morphometric approaches and multivariate analyses. Our results revealed a considerable heterogeneity in cranial morphology. The two species appeared to be clearly differentiated although sympatric populations were closer to each other and had a slight overlap in the morphometric space. Within M. eversmanii, the subspecies and the nominal taxon only partially overlapped, and M. eversmanii eversmanii was more distant from M. putorius than subspecies hungarica. Although morphometric analyses revealed several intermediate individuals in size in sympatric M. eversmanii and M. putorius populations, only a small fraction of such specimens showed conflict in discrete morphological characters with the diagnostic discriminant function. We interpret these results as an indication of ongoing hybridisation between sympatric populations, but the low number of hybrids identified suggests limited genetic exchange between the species.