Stipa capillata L. (Poaceae) is a rare grassland species in Central Europe that is thought to have once been widespread in post-glacial times. Such relict species are expected to show low genetic diversity within populations and high genetic differentiation between populations due to bottlenecks, long-term isolation and ongoing habitat fragmentation. These patterns should be particularly pronounced in selfing species. We analysed patterns of random amplified polymorphic DNA (RAPD) variation in the facultatively cleistogamous S. capillata to examine whether genetic diversity is associated with population size, and to draw initial conclusions on the migration history of this species in Central Europe. We analysed 31 S. capillata populations distributed in northeastern, central and western Germany, Switzerland and Slovakia. Estimates of genetic diversity at the population level were low and not related to population size. Among all populations, extraordinarily high levels of genetic differentiation (amova: φST = 0.86; Bayesian analysis: θB = 0.758) and isolation-by-distance were detected. Hierarchical amova indicated that most of the variability was partitioned among geographic regions (59%), or among populations between regions when the genetically distinct Slovakian populations were excluded. These findings are supported by results of a multivariate ordination analysis. We also found two different groups in an UPGMA cluster analysis: one that contained the populations from Slovakia, and the other that combined the populations from Germany and Switzerland. Our findings imply that S. capillata is indeed a relict species that experienced strong bottlenecks in Central Europe, enhanced by isolation and selfing. Most likely, populations in Slovakia were not the main genetic source for the post-glacial colonization of Central Europe.