A highly selfing breeding system affects gene flow, which may have consequences for patterns of genetic variation and differentiation on both the population and species level. Feather grasses (Stipa spp.) are dominant elements of Eurasian steppes that persist in Central Europe in scattered isolated populations that are of great conservation interest. Cleistogamy is common in the Stipa pennata group, the phylogeny of which is largely unresolved. Intraspecific patterns of genetic variation can be characterised by lack of gene flow due to selfing, but also by large-scale historical migrations and long-term isolation. We analysed both 5 species within the S. pennata group and 33 populations of Stipa pulcherrima sampled across a large part of its range. Using AFLP markers we assessed phylogenetic relationships of the S. pennata group and patterns of genetic variation within and among populations. The S. pennata group formed a consistent clade separated from S. capillata. Stipa pulcherrima was sister to S. eriocaulis, but the relationships among S. pennata s. str., S. borysthenica., and S. tirsa remained unresolved. Within-population genetic variation was extremely low in all species of the S. pennata group (H_e = 0. 0-0. 013). In S. pulcherrima, genetic variation was consistently relatively high in the east (Romania, Russia) and declined toward western populations, with many populations at the western range edge lacking genetic variation entirely. Populations were strongly differentiated (F_ST = 0. 762), and this differentiation did not follow a classical pattern of isolation by distance. Bayesian cluster analysis revealed nine gene pools in S. pulcherrima, which were mostly geographically clustered. Overall the results suggest that S. pulcherrima and species of the S. pennata group are characterised by a cleistogamous breeding system leading to extremely low levels of genetic variation and high levels of population differentiation at both the population and species level. Postglacial colonisation, current population isolation, and population bottlenecks at the western range periphery have further reduced genetic variation and obviated gene exchange. Thus, genetic variation can only be preserved by the conservation of multiple populations.