Six metal-tolerant populations and sub-populations of Armeria maritima ssp. halleri, ssp. hornburgensis, and ssp. botten-dorfensis and two non-tolerant populations of ssp. elongata in Central and Northeast Germany have been analysed using RAPID markers. The populations show very strong genetic differentiation ((Phi(ST) = 0.46), corresponding gene flow between them is low (N(e)m = 0.29). A moderate positive correlation between the matrices of genetic and geographical distances was found between the seven populations and sub-populations of central Germany (r = 0.68, p < 0.001). Calculated parameters of genetic variability are molecular variance, percentage of heterozygosity and percentage of polymorphic loci. A significant correlation between population size and parameters of genetic variability was not recognisable. Genetic structure was investigated by an analysis of molecular variance (AMOVA). The studied populations show strong genetic differentiation. Genetic variation within populations ("normal" as well as metalliferous) is higher (53.9%) than among them (46.1%). Six hypotheses of possible genetic relatedness between the studied populations have been tested by AMOVA. A data set structure above the populational level is hardly recognisable. It was impossible to combine the populations to edaphic (tolerant and "non-tolerant") or taxonomic groups. A. maritima ssp. halleri of the north Harz mountains and ssp. hornburgensis are clearly separated from a geographical group containing all other populations (across taxonomic and eclaphic boundaries). These results are a further indication for a polyphyletic origin of metal-tolerant populations of A. maritima s.I. by multiple colonizations of metalliferous sites from neighbouring populations on non-metalliferous soil.