Five populations of eelpout Zoarces viviparus from the White Sea, the Baltic (Gulf of Gdansk and Gulf of Finland) and the North Sea (Wadden Sea and Hafrsfjord) were studied. Using 17 bilateral meristic characters (number of holes in cranial bones) we assessed the following parameters: (i) fluctuating asymmetry (minor deviations from perfect bilateral symmetry), (ii) the factorial component of total phenotypic variance, which is a measure of within-population heterogeneity and (iii) mean values of each character. Morphological similarity among samples was only weakly correlated with geographical distances between sample locations. The magnitude of fluctuating asymmetry was higher in the samples from the White Sea and Hafrsfjord than in samples from the Wadden Sea and the Baltic Sea. The sample from the Gulf of Gdansk was characterized by the lowest fluctuating asymmetry and the highest factorial variation. We propose that among the most important factors determining fluctuating asymmetry in eelpout populations are salinity and temperature conditions and the level of genetic variation.