We investigated the genetic variability within and among populations and the breeding system, germination and seedling survival in the remaining populations of the endangered Typha minima along the upper River Rhine. Isozyme analysis revealed low genetic differentiation among populations (mean genetic distance, D=0.03). However, the mean number of alleles per locus differed among populations, and the number of different multilocus genotypes per population, which varied between one and 18, increased with increasing population size. Successional habitat stage characterised the spatial distribution of individual clones within populations. Spontaneous self-pollination resulted in a 23% lower seed set than spontaneous cross-pollination or open-pollination, suggesting a mixed mating or even outcrossing breeding system. Experimental germination of seeds of T. minima decreased with increasing storage from 90.4% after 5 months to 43.6% after 8 months and to zero after 16 months. No seedlings could establish in populations of later successional stages. For the conservation of T. minima along the upper River Rhine, the remaining populations should be preserved, and re-introduction of ex situ cultivated plants to suitable habitat patches might restore population connectivity and increase the possibility of spontaneous colonisation.