Analyses of intraspecific genetic structure can promote the conservation of genetic diversity of rare or declining plant species by enabling identification of proper management units. Here we investigate the genetic structure of the annual hemiparasitic herb Rhinanthus angustifolius to evaluate the genetic distinctness of two currently described subspecies and three habitat-related groups of populations inferred from recent common-garden data. Data from 11 nuclear microsatellite loci, obtained from 17 southern Swedish populations of R. angustifolius, were analyzed with a variety of population genetic techniques to examine how intraspecific genetic structure relate to taxonomy, habitat and geography. Neither the two subspecies nor the three recently identified population groups formed genetically coherent lineages. Rather, there was a clear isolation-by-distance pattern, pointing to a major role of geographically restricted gene flow in structuring the diversity at the putatively neutral microsatellite loci. Although uncertainties remain regarding the influence of homoplasy and possible introgression from the closely related R minor, our microsatellite data argue against the recognition of previously identified subspecies or population groups as management units for conservation purposes. As currently described entities do not contain much unique genetic variation, we recommend conserving populations from a large geographical range, rather than populations from specific habitats, to preserve the long-term evolutionary potential of the species.