Angelica palustris (BESSER) HOFFM. (Apiaceae) is a rare wetland community species that is currently rapidly declining because of changes in land use. In the present study, we analyzed patterns of random amplified polymorphic DNA (RAPD) variation among nine populations of A. palustris in Germany to assess its overall genetic condition. We aimed to examine the level of genetic diversity as well as its local differentiation in relation to population size and geographic distancing between populations. Results achieved from φ_ST statistics and AMOVA indicated that most of the variability is distributed among individuals within the populations (57.7%), whereas among-population variation accounted for 30.2% of the variation. Variation between regions was 12.1%. This corresponds to the results of a multivariate analysis based on the asymmetric Soerensen similarity, which also suggested a strong population differentiation, as would be expected from a short-lived species with limited seed dispersal capacities that had never covered extensive areas in Eastern Germany. Consistently the geographic differentiation was not reflected in the RAPD profile. Significant correlations were noted between population size and the percentage of polymorphic loci (P < 0.05) and genetic diversity (P < 0.05). An analysis of seed production showed positive relationships between average seed number and levels of genetic variation. Our results support concerns regarding the loss of genetic diversity in endangered plant populations because this process might have harmful effects on reproductive fitness.