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Understanding the processes that determine genetic variation within landscapes is a crucial factor for successful management of threatened plant species that are sensitive to both environmental and genetic bottlenecks. While current insights point to the importance of historical landscape processes for the genetic structure of populations at large spatial scales, their relevance at small spatial scales has been largely neglected. In this context, coastal dunes are a typical example of dynamic and geologically young landscapes in which current and historical sand drift may have strong impacts on the spatial dynamics of a large number of plant species. One of these is the endangered plant species Parnassia palustris, typically inhabiting dune slacks formed by recent sand displacements in parabolic dune landscapes. Dune slacks originating from the same sand drift process are located within the same parabola unit. The species is known to suffer from dispersal limitation and from inbreeding when genetic exchange between populations is restricted. By means of amplified fragment length polymorphism, we demonstrate that the species shows a genetic substructuring both at the level of the metapopulation and the local landscape. Populations located within the same parabola unit are much more closely related than expected on the basis of geographic distance. Moreover, population size is related to genetic diversity within populations. The species' population genetic structure should consequently be regarded as a shifting mosaic of genetic variation, mediated by sand drift driven landscape formation. Therefore, the maintenance of sand dynamics is essential to preserve genetic diversity in dynamic dune landscapes. [ABSTRACT FROM AUTHOR]