Taxonomic analyses of four Sabanejewia balcanica populations from Croatia included morphological (morphometric, meristic, phenotypical) and mitochondrial DNA analyses. Comparative analyses of 24 morphometric characters revealed some differences between populations. The specimens from the Drava River are significantly larger than specimens from other populations, whereas the individuals from the Voćinska River represent the smallest European S. balcanica specimens. Due to similarities in morphometric ratios, in the Tree Diagram of Euclidean distances, the Drava and Petrinjčica Rivers populations formed a separate cluster, while the populations from the Rijeka and Voćinska Rivers formed a second cluster. These morphometrical differences are also corroborated by t-test results. Differences among fishes from different populations also exist in external morphology characters, such as spots on the caudal peduncle and the position of the suborbital spine. Mitochondrial DNA analyses enabled us to infer the phylogenetic placement of four Croatian populations within the genus Sabanejewia. All Croatian samples clustered within the two sublineages of the Danubian-Balkanian complex. Samples from the Voćinska River, as well as one sample from the Drava River were included in the “S. balcanica” (VI) sublineage. The remaining samples, including the two remaining haplotypes from the Drava River, were comprised within “S.montana-S.bulgarica-S.balcanica” (III) sublineage.