The diversity of Croatian ichthyofauna, considering the richness of species and endemic species, places Croatia among one of the ichthyologically most populous countries of Europe. Species richness is a result of the geological past, isolation of Adriatic rivers basin and geographical position, which includes two river drainage basins: The Adriatic and the Black Sea basin. Seven populations of genus Rutilus were processed: three R. aula populations, two R. basak populations, one R. rutilus population and one R. virgo population. The objectives of this research were to determine for the first time in Croatia the basic morphological characteristics of the mentioned Rutilus species and to describe the diversity between the same and different populations among species. Morphometric and meristic features were determined on 96 samples. After standardization, morphometric features were compared using analysis of variance (ANOVA) and principal component analysis (PCA). PCA of standardized morphometric characters clearly showed population grouping while PCA of non – standardized morphometric characters resulted in population overlapping. Interestingly, geographically distant populations of the R. aula species showed more similarities than those geographically close. R. virgo population showed the widest morphometric and meristic variability. The results of the morphometric analysis have shown interpopulational and intrapopulational variability. Finally, the results of this research represent a significant contribution to the knowledge of the morphology of the genus Rutilus in Croatia and may be useful for future research.