Calamagrostis pseudopurpurea is one of only a few endemic species in Germany and is confined to the catchment area of the River Mulde in the states of Saxony and Saxony-Anhalt. We studied the genetic structure and seed viability across its entire distribution area. Patterns of random amplified polymorphic DNA (RAPD) variation were analysed using 183 individuals from 43 stands in order to assess the overall genetic structure and the extent of clonality. In addition, four related Calamagrostis species (C. canescens, C. epigejos, C. phragmitoides and C. villosa) were included in our study to consider the probable phylogenetic origin of C. pseudopurpurea. We detected two clearly different RAPD phenotypes of C. pseudopurpurea, each distributed along the river banks of two spatially isolated stream courses. Both phenotypes are present downstream of the confluence. Our results indicate that C. pseudopurpurea originates from two distinct periods of hybridisation between the same parental taxa, and that clonal propagation is most likely the main reproduction method. In line with its hybrid origin, embryos of sampled C. pseudopurpurea caryopses were found to be mostly degraded or unviable over several years. Calamagrostis pseudopurpurea is genetically closer to C. canescens and C. phragmitoides than it is to other studied species, but C. canescens and C. phragmitoides have not been proven to be direct parental taxa of C. pseudopurpurea. Calamagrostis pseudopurpurea should therefore still be treated as a separate species that needs special attention from a conservation point of view.