The MiSeq run yielded ~14*106 sequences for the Iberian DNA pool and ~20*106 for the Baltic one. The genome assembly amounted to 148 601 contigs in ~ 236*106 bases, with an N50 of 1425 of which we could isolate primers for 4453 microsatellite loci. We genotyped populations across the European range of the yellow sac spider (Fig. 1A) for 14 of these loci. This revealed significant genetic structure. Our STRUCTURE analysis suggested k = 3 populations. We found a homogeneous native European population, including samples from the Iberian Peninsula, Italy, Slovenia, southwestern Germany and Russia (Fig. 1B). In contrast to the homogeneity in the native range, we identified two genetically separated expanding populations: one in the Baltic States and another in the northeastern German state of Brandenburg. The northeastern German populations were less divergent in comparison with the native cluster than the Baltic ones (allele frequency difference Baltic versus. Native = 0.045, allele frequency difference NE‐Germany versus Native = 0.022). Moreover, the two expanding clusters were clearly divergent (allele frequency difference Baltic versus NE‐Germany = 0.034). A second STRUCTURE analysis excluding the two expanding populations suggests additional and finer‐scaled genetic structure in the native European cluster with k = 2. Eastern and western European populations from Russia and the Iberian Peninsula each form separate clusters. The eastern cluster extends to the Balkans and southwestern German, while populations from Italy appear admixed between these two clusters (Figure S2). These results were generally supported by an allele sharing phylogeny of the data with the expanding population from northeastern Germany and the Baltic States forming well‐separated clades. The phylogeny also suggested a similar differentiation of Russian and Iberian populations within the native range, with other native populations grouping between these two (Figure S3). An analysis of F ST differentiation between populations additionally confirmed our previous analyses. The two expanding populations were divergent from each other and all native populations, while the differentiation between native populations was considerably lower (Table 1).