BACKGROUND AND AIMS: The dwarf eelgrass, Zostera noltii, is a predominant inhabitant of soft-bottom intertidal regions along the coasts of northern Europe. It is a monoecious, protogynous angiosperm in which the potential for self-fertilization and inbreeding are high, especially if clone sizes exceed pollen dispersal distances. The aim of the present study was to determine the relationship between mating system and clonal structure, examine the relative roles of geitonogamous selfing and biparental inbreeding, measure pollen availability (multiple paternities) and estimate pollen dispersal. METHODS: A 100-m(2) plot was established in a large, intertidal Z. noltii meadow on the island of Sylt in the German Wadden Sea. A total of 256 adult shoots was sampled: one from the centre of 100 fixed 1-m(2) quadrats (large scale resolution) and an additional 156 from within eight randomly selected 1-m(2) sub-quadrats (small-scale resolution). DNA was extracted from seeds and leaf tissue of all samples and genotyped with nine microsatellite loci. KEY RESULTS: Mating system analysis revealed high multilocus and single locus outcrossing rates. Average pollen dispersal distance was nearly the same as the average genet (clone) size. Multiple paternity was common and 20-30 % of mature seeds originated from matings within the plot. Among inbred seeds, most resulted from geitonogamy rather than biparental inbreeding. CONCLUSIONS: Moderate disturbances intrinsic to the intertidal habitat appear to facilitate seed recruitment by gap formation. Pollen dispersal distances are sufficient to maintain outcrossing and high clonal diversity.