We assessed the genetic variability of the Siberian spined loach Cobitis melanoleuca across its unusually broad distribution that encompasses areas greatly affected by Pleistocene glaciations. Due to extensive morphological variation among their populations, the taxonomic status of C. melanoleuca is complicated. It is unclear whether C. melanoleuca represents a single taxonomic unit or contains several species or subspecies. Our analyses showed low genetic variability in all populations without any phylogenetic structure. The absence of molecular distinctiveness indicates the conspecificity of all C. melanoleuca populations. Only a few common haplotypes shared by East Asian, Siberian and European populations were found at high frequency in the nuclear genes analysed. At the mitochondrial level, Siberian populations shared haplotypes with populations located at both extremes of the species’ range suggesting central populations as a source of current mitochondrial variability. Unimodal mismatch distributions and significant values from neutrality tests support a recent expansion of C. melanoleuca. Our time estimates suggest a postglacial colonisation of European waters around 1.0 MYA, indicating that C. melanoleuca may represent the last cobitid immigrant in Europe that used the northern route across Siberia to expand its range.