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Background  The zooplanktonic cladocerans  Daphnia , present in a wide range of water bodies, are an important component of freshwater ecosystems. In contrast to their high dispersal capacity through diapausing eggs carried by waterfowl,  Daphnia  often exhibit strong population genetic differentiation. Here, to test for common patterns in the population genetic structure of a widespread Holarctic species,  D. galeata , we genotyped two sets of populations collected from geographically distant areas: across 13 lakes in Eastern China and 14 lakes in Central Europe. The majority of these populations were genotyped at two types of markers: a mitochondrial gene (for 12S rRNA) and 15 nuclear microsatellite loci.    Results  Mitochondrial DNA demonstrated relatively shallow divergence within  D. galeata , with distinct haplotype compositions in the two study regions but one widely distributed haplotype shared between several of the Chinese as well as European populations. At microsatellite markers, clear separation was observed at both large (between China and Europe) and small (within Europe) geographical scales, as demonstrated by Factorial Correspondence Analyses, Bayesian assignment and a clustering method based on genetic distances. Genetic diversity was comparable between the sets of Chinese and European  D. galeata  populations for both types of markers. Interestingly, we observed a significant association between genetic distance and geographical distance for  D. galeata  populations in China but not in Europe.    Conclusions  Our results indicate relatively recent spread of  D. galeata  across wide expanses of the Palaearctic, with one mtDNA lineage of  D. galeata  successfully establishing over large distances. Despite a clear differentiation of Chinese and European  D. galeata  at a nuclear level, the pattern of genetic variation is nevertheless similar between both regions. Overall, our findings provide insights into the genetic population structure of a cladoceran species with extremely wide geographical range.    Electronic supplementary material  The online version of this article (10.1186/s12862-018-1256-4) contains supplementary material, which is available to authorized users.

Cytonuclear diversity and shared mitochondrial haplotypes among Daphnia galeata populations separated by seven thousand kilometres