The invasion of Ponto-Caspian taxa in Western Europe has increased steadily since the connection of the Danube basin with the Rhine basin in 1992, in combination with transfers through interbasin shipping. In 2010, the tubenose goby (Proterorhinus semilunaris) and round goby (Neogobius melanostomus) were observed in Belgium for the first time. To gain insight in the introduction pathways in Belgium and to identify potential source populations, a phylogeographical and parasitological study was initiated on both species. The mitochondrial cytochrome b gene was sequenced, its haplotype diversity calculated and a statistical parsimony haplotype network built. Both species exhibited low haplotype diversity compared to native and other non-native populations. The network revealed potential source locations in the Northern Black Sea for the round goby and in the Danube at the Serbian-Romanian border for the tubenose goby. Fins, gills and body were examined for the presence of ectoparasites. Prevalence, abundance and infection intensity was much higher in tubenose goby, which might be the consequence of a different introduction pathway. Our data provides evidence that tubenose goby entered Belgium through active dispersal. The round goby, however, was most likely introduced with ballast water.