Former and present cultivation of plant species impacts their distribution patterns and today's composition of floras. If native and feral populations are overlapping, the local status of a species remains often questionable. The musk strawberry (Fragaria moschata) is such an example: It is native to Central Europe but has been extensively cultivated until the end of 19th century. The border between native and synanthropic distribution runs presumably from Northeastern to Southwestern Germany. To analyse the relationship between native and synanthropic populations of F. moschata, we performed a population genetic analysis using seven microsatellite markers: We compared native populations from Germany and the Czech Republic, proposed synanthropic occurrences from Germany and cultivars of F. moschata from the germplasm repository "Professor Staudt Collection". Synanthropic populations were genetically less diverse than native ones and consisted often of one clone only. The results revealed four clones frequently found in synanthropic populations across Germany and moreover, we detected a clear genetic separation between synanthropic and native populations. Furthermore, synanthropic populations were differentiated in a Northern and a Southern German cluster, each comprising cultivars of Northern or Southern European origin as well. We conclude that the synanthropic populations in Germany were actively spread by humans. Dispersal of these populations is extremely limited due to fragmentation and the lack of mating partners. Synanthropic populations were not established by collecting nearby native occurrences but are rather related to different cultivation centres in Europe.