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 River Timok (eastern Serbia) and all River Sava populations. The only locality that housed haplotypes of both clusters was 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).