The aim of this study was to examine morphometric differentiation of gudgeon (Romanogobio and Gobio) species inhabiting the Carpathian Basin, Hungary, with special regard to two recently described species classified into the Gobio genus. For statistical analyses, 23 morphometric and 8 meristic characters were measured on each of the 733 preserved specimens originating from museum collections. The analyses of the standardized morphometric traits revealed low intraspecific variability in all studied species, but varying degrees of interspecific differences. The strongest morphometric differentiation was found in Romanogobio uranoscopus (Agassiz, 1828), which can be characterized by the most special environmental needs. The two allopatric Gobio species showed the weakest morphometric difference. The meristic characters showed high variability in the Romanogobio spp., but did not show significant differences in the two Gobio species. The results show that the morphometric and meristic similarity of the studied Gobio species is definitely high, which preclude reliable identification based on phenotypic characters if only some specimens are available. It seems that the most usable discriminating feature for these species is the localization of the collection site.