In mid-1990s racer goby (Babka gymnotrachelus) penetrated to the Vistula and Western Bug rivers in Poland through the canal connecting the Baltic and the Black Sea basins, namely the Vistula and Dnieper drainages. In early 2000s, the species was reported from Polish section of the Strwiąż River that is an affluent of the Dniester River that drains to the Black Sea basin. According to the Polish legislation, the racer goby has been enlisted in as an alien invasive species that may pose threat to local biota. Our analysis of the mtDNA cytochrome b diversity revealed that the Vistula/Western Bug and Strwiąż populations are different genetic units. First one originated from the Dnieper River, while the second derives from the Dniester River. According to the results of mismatch analysis, both are in the stage of demographic and spatial expansion. The haplotype frequencies in population from the Vistula/Western Bug differ significantly from those in the source population in Dnieper, suggesting founder effect, possibly due to human-mediated introduction of low number of individuals. On the other side, the population in Strwiąż does not differ in structure from the one in Dniester, providing a hint towards spontaneous range expansion. Interpretation of our results in light of historical data lead to the conclusion that presence of racer goby in Strwiąż was probably overlooked in previous, spatially limited, studies. Thus, in Strwiąż the species should not be treated as alien, contrary to its status in the Vistula drainage. This double origin of racer goby populations in Poland creates a peculiar situation for national legislation procedures as one population is alien and invasive, while the other one is not. In light of our findings, the population from Strwiąż should be recognised as a special case. Steps should be undertaken to raise public awareness to prevent translocation of the gobies between the rivers to prevent deterioration of the evolutionarily isolated genetic pools of the Dnieper and of the Dniester basins. Our results illustrate the need for case studies upon genetic population structure, following appearance of new species in previously unoccupied water bodies, even on local scale.