In urban river systems, fragmentation of habitats and in-stream dispersal barriers play a major role in shaping the population genetic structure of freshwater macroinvertebrate species. In small, fragmented populations, effects of genetic drift and inbreeding are enhanced, which can lead to increased population differentiation and genetic diversity loss. One formerly strongly degraded and fragmented stream system in a highly urbanised area is the Emscher catchment in North Rhine-Westphalia, Germany. Major restoration efforts have led to an improvement of water and habitat quality over the past 20 years also in the formerly polluted tributaries, for example, the Boye catchment. However, the analysis of the population structure of two different amphipod and isopod species has revealed that some populations are still strongly isolated, indicating persisting gene flow barriers. In contrast, the effects are expected to be less pronounced in merolimnic species, which have an adult winged life stage, such as the alderfly Sialis lutaria (Linnaeus, 1758) . However, this species was much less abundant in the Boye catchment and not found in adjacent catchments (only 9 of 41 sampling sites), reducing the power of possible analyses.<br> As no population genetic studies of S. lutaria have to our knowledge been published so far and genetic resources are generally scarce for this species, we generated and present here population genetic data for 70 S. lutaria specimens for the mitochondrial cytochrome c oxidase I (COI) gene and, more importantly, high resolution genomic single nucleotide polymorphism (SNP) data for 71 specimens, generated with double-digest restriction site-associated sequencing (ddRAD-seq). These data can be valuable for further studies, analysing the population genetic structure, dispersal pathways and potential gene flow barriers for S. lutaria on a larger geographic scale. Additional to presenting the data, we also give first insights in the population structure on a small geographic scale (area of approx. 15 km2). While the population differentiation was generally low, as expected on this small scale, we still found that gene flow was not equally strong between all populations, but that one population played a central role as a source and sink population, which cannot only be explained by the distance between populations.
