Deschampsia littoralis is an endemic tetraploid Poaceae occurring on the shores of pre-Alpine lakes. It is closely related to the diploid and widespread D. cespitosa. Several D. littoralis populations from Lake Constance are vegetatively propagating through pseudoviviparous spikelets. These latter populations were formerly described as a separate species, D. rhenana. Still, the species status of D. rhenana has been questioned since, apart from pseudovivipary, no morphological differentiation from D. littoralis is observed. Both species are highly endangered and accurate assessment of taxon status is needed for conservation management. We used amplified fragment length polymorphism fingerprinting to assess whether D. rhenana from Lake Constance (43 specimens) was genetically differentiated from D. littoralis (11 specimens collected at Lac de Joux, incl. Lac Brenet) and the widespread D. cespitosa (48 specimens). An analysis of molecular variance (AMOVA) showed that 12 % of the genetic diversity occurred among the three species, 7 % occurred among populations within species and 81 % within populations. Principal coordinate analysis and fuzzy c-means clustering showed that D. rhenana was genetically distinct from D. littoralis. In addition, both species differed in levels of genetic diversity and clustering, with D. rhenana being the most divergent and structured species. D. littoralis appeared as genetically intermediate between D. rhenana and D. cespitosa. These results suggested that (1) all species are closely related, (2) genetic variation within populations is high even in the asexually propagating D. rhenana and (3) D. rhenana is more distinct from D. cespitosa than is D. littoralis. We therefore suggest to treat D. rhenana from Lake Constance and D. littoralis from Lac de Joux as independent evolutionary units in conservation management.