The genetic structure of Chaoborus flavicans was analyzed to start an investigation of the evolutionary status of this Holarctic species and to make inferences about C. flavicans' historical distribution and dispersal. We sequenced a 611 bp fragment of the cytochrome oxidase subunit I and II gene for 26 populations spread across Europe and North America. We found distinct North American and European C. flavicans clades. Chaoborus crystallinus, widely accepted as a sister species of C. flavicans, clustered within the European C. flavicans clade, suggesting potential peripatric speciation. The genetic relationship of the C. flavicans haplotypes within Europe suggests that several glacial refugia existed during the last ice age in southern Europe. European C. flavicans recolonized central and northern Europe from refugia in France and/or Spain after glaciers retreated. This phylogeographic structure was roughly comparable to that of other zooplankton species. The correlation between genetic and geographic distance within Europe was significant, indicating that short distance dispersal in C. flavicans is more common than in other passively dispersing zooplankton species.