The sea aster, Aster tripolium L., grows naturally in temperate regions, mainly in the salt meadows close to the coast. The species is also found in naturally and anthropogenically salt-contaminated inland habitats, such as potash mine dumps. The genetic relationships among populations from different habitats and correlations of the genotype with physiological and vegetational parameters were investigated. A. tripolium plants from five different sites close to the seashore on the North Sea island Baltrum, from five different potash mine dumps and, as an outgroup, from the seashore in Japan were probed. DNA was extracted from five plants from each of the 11 A. tripolium populations and analyzed for random amplified polymorphic DNA (RAPD). Altogether 35 polymorphic bands in 51 individuals and 45 different detectable genotypes could be identified. For evaluation of the genetic variation using RAPD bands, the neighbor-joining method, the principal coordinate analysis, and the analysis of molecular variance were applied, resulting in the classification into three genetic groups. A. tripolium plants from different ecological habitats on Baltrum were closely related while the plants growing at the deposit dumps showed a higher genetic diversity. The Japanese population was genetically very different from the German populations. Correlations between phytosociological and soil parameters and the respective genotype were not significant. The results argue for a conservation of anthropogenically salt-contaminated habitats to maintain genetic variability not only on the species level, but also within a species.