Three small populations of the rare allopolyploid peat moss species Sphagnum troendelagicum are studied using RAPD markers. Contrary to expectations, levels of neutral genotypic and haplotypic variation are moderately high in this seemingly asexual species. A model is presented for estimating relative impact of recombination on genetic variability. Recombinations appear to occur rarely in studied populations compared to mutation events, even though little significant linkage disequilibrium exists. We hypothesize that multiple origins of the species due to recurrent hybridization events may partially account for the observed variability.