Physical disturbance by large herbivores can affect species diversity at the community level and concurrently genetic diversity at the species level. As seedling establishment is rarely observed in clonal plants, short-term experiments and demographic studies are unlikely to reveal the response of clonal plants to disturbances. A long-term (30-year) field experiment and the availability of molecular markers allowed us to investigate the clonal structure of populations of Elytrigia atherica subjected to different management regimes. The long-term field study provided us with five replicated blocks that had been subjected to three different management regimes, grazing by cattle, mowing and abandonment. In this study we examined the effects of herbivore grazing and mowing on clonal richness and genetic diversity of populations in salt marshes using multilocus microsatellite genotypes. In addition, phenotypic traits and spatial positions of E. atherica ramets were determined for 20 samples in a 5 × 10m plot in each of the blocks. Abundance and phenotypic traits were affected by the management regimes, resulting in a higher abundance in abandoned fields and plants having shorter and narrower leaves in managed fields. Biomass removal did affect the clonal structure of populations and increased the genetic diversity compared to that in abandoned fields. However, no distinct difference was found between the two management regimes, mowing and grazing. Although seedling recruitment has rarely been observed, the present study shows that such rare events have occurred within the populations studied. Thus, molecular tools can greatly increase our understanding of vegetation dynamics and processes within populations growing under different conditions.