The ecological importance of scattered tree species such as elms (the European white elm, the wych elm and the field elm) is widely recognized in Europe. The European white elm, along with other elm species, is important as part of the traditional landscape and as a tree with multiple uses. In Germany, a total of more than 825 white elm populations numbering approximately 138,000 trees have been inventoried. Most of the largest populations are closely associated with the main rivers and concentrated mainly in the northeast of the country. However, to date there has been a lack of knowledge on the genetic structure and diversity of European white elm populations in Bavaria (southern Germany). The aim of this study was to assess genetic structure and diversity and to select putative seed stands and gene conservation units (GCU) for European white elm. Nuclear microsatellite loci (nSSR) were first selected for successful elm species discrimination. Next, in order to represent the distribution range of European white elms in Bavaria, 18 populations were selected and sampled for genetic analysis with 12 variable nSSR loci. AMOVA revealed that genetic variation is mainly distributed within populations (89%), while only 11% occurred between them (F_ST = 0.11). Bayesian clustering indicated the highest probability for the presence of four genetic clusters (Delta K = 19.954 at K4) within the dataset. However, spatial genetic structure indicates a close link to the two main river basins in Bavaria (Main River basin and the Danube River basin). Thus, our results fill existing gaps in sustainable use and conservation of rare and scattered tree species by providing insights into genetic variation and genetic structure of the species and allow us to better plan genetic conservation measures and to select GCU and seed stands in Bavaria. We, therefore, suggest that in the future all putative seed stands or gene conservation units should be assessed based on several aspects, one of them being the level of genetic diversity, before final selection and use as a source of forest reproductive material (FRM).