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Zooplanktonic organisms that disperse passively as diapausing eggs often exhibit surprisingly strong population subdivision given their high colonization ability. Here we attempt to disentangle the impacts of colonization history and gene flow on these organisms by studying the population genetic structure of the rotifer Brachionus plicatilis. The resting egg banks of B. plicatilis in fourteen salt lake populations in the Iberian Peninsula were examined using seven microsatellite loci. A remarkably high degree of geographical structuring was found (Fst = 0.43), with a significant pattern of isolation by distance. Microsatellite loci were in genetic equilibrium, ruling out inbreeding as an important force in population structuring. Comparisons are drawn with previously published phylogeographical data. Surprisingly, introgression of nuclear genes was detected in neighbouring populations with divergent mtDNA haplotypes. These results stress the long lasting impact of colonization history and the modulating effect of gene flow at local scales in these organisms.