A special feature of spined loaches of the genus Cobitis in Central Europe is the frequent occurrence of diploid-polyploid complexes in which polyploid gynogenetic forms act as sperm parasites to the diploid form. This tight binding of the co-occurring forms results in a high level of phenotypic and ecological similarities. The present study searches for morphological differences between them applying the characters traditionally used in loach taxonomy (body proportions, fin formula, scale shape, lamina circularis, suborbital spine, coloration) in 662 specimens from the Baltic (14 populations) and North Sea (1 population) catchment areas. Ploidy level of each specimen was inferred from blood cell measurements. Discriminant function analysis for biometrical characters and description of qualitative features indicate the morphological distinctness of the two diploid species C. taenia and C. elongatoides. The polyploid unisexual biotypes are very similar to each other and to individuals of sympatric sexual species. The genome dosage effect could be observed in morphological characters, however, in some of them the polyploid biotypes display a mosaic mode of variability: they can be more similar to sympatric parents or to the absent species in the complex, transitional and of a wider variability range. In colouration pattern, the biotypes do not express the whole spectrum of the parental species variability. Meristic traits had no power to identify the different forms.