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We analysed the pattern of genetic differentiation among six newly established (around 10 generations) sites of the round goby (Neogobius melanostomus) in the southern Baltic Sea by means of nine microsatellite loci and in total 183 individuals. All but one site were within 30 km from each other. We found statistically significant genetic differentiation in ten out of 15 comparisons after Bonferroni correction, and since the species is newly introduced this has happened in less than ten generations. The largest genetic differentiation was found between the two most divergent habitats, while sites with a similar habitat were not significantly differentiated. Estimates of gene flow (Nm) were low and ranged from 1.5 to 5.5. A large proportion of individuals were assigned to one site (Puck), suggesting that this site has acted as a source to the other sites.