Inter-population variability within Sabanejewia populations from the western Balkans, and their phylogenetic position in comparison to other European populations were investigated. Of 79 samples analysed, 51 unique haplotypes were identified. Network analysis divided thirteen populations from five river basins into two clusters: cluster I was composed of populations from the Vardar drainage and tributaries of the neighbouring River Morava (River Danube basin), while cluster II contained the River Timok (eastern Serbia) and all the River Sava populations. The only locality that housed haplotypes of both clusters was the River Kutinska reka in the upper Morava basin. When compared with the haplotypes reported in former studies, both clusters fell within the ‘Danubian-Balkanian complex’. Cluster II was included in the most heterogeneous sub-lineage S. montana – S. bulgarica – S. balcanica (III), while cluster I was related to the sub-lineages S. doiranica – S. balcanica (II) and S. balcanica (VI). Recently published haplotypes from the Croatian Sava (rivers Petrinjčica and Rijeka) and Drava (rivers Drava and Voćinska) basins, as well as Czech and Slovak individuals from the Danube and Tisza river basins were included. The River Drava showed the same population subdivision as the River Kutinska reka.