Repeated invasions of European waters by the ctenophore Mnemiopsis leidyi offer a unique opportunity to study population dynamics and dispersal in gelatinous zooplankton. Here we followed population establishment in 2 recently invaded areas, the North and Baltic Seas, and analysed changes in population structure during a 3 yr interval using 7 highly polymorphic microsatellites comprising 191 alleles. A second goal was to reconstruct routes of recent invasive range expansion into the Mediterranean Sea. During the study period (2008 to 2010), populations in the North Sea and Western Baltic Sea maintained their allelic composition with virtually unchanged levels of genetic diversity and between-population differentiation, demonstrating limited gene flow between the 2 regions and successful reproduction in both areas. In contrast, at the eastern distribution limit in the central Baltic (Bornholm Basin), the same measures fluctuated between years and genetic diversity decreased from 2008 to 2010. In concordance with prior ecological observations, this supports the view that M. leidyi in the central Baltic is a sink population. In the area of recent range expansion (Mediterranean Sea), we observed high population differentiation: pairwise differentiation (F ST ) values between sites in Spain, France and Israel were significant and between 0.04 and 0.16. Despite this differentiation, Bayesian clustering and phylogeographic analysis support the hypothesis that all Mediterranean M. leidyi result from a secondary introduction originating from the Black Sea. Our study contributes to growing evidence that multiple invasions of the same species can vary in their degree of genetic diversity and demonstrates how genetic markers can help to resolve whether gelatinous plankton species form self-sustaining populations.