The persistence of tidal wetland ecosystems like salt marshes is threatened by human interventions and climate change. In particular, the threat of accelerated sea level rise (SLR) has increasingly gained the attention of the scientific community recently. However, studies investigating the effect of SLR on plants and vertical marsh accretion are usually restricted to the species or community level and do not consider phenotypic plasticity or genetic diversity. To investigate the response of genotypes within the same salt-marsh species to SLR, we used two known genotypes of Elymus athericus (Link) Kerguélen (low-marsh and high-marsh genotypes). In a factorial marsh organ experiment we exposed both genotypes to different flooding frequencies and quantified plant growth parameters. With increasing flooding frequency, the low-marsh genotype showed higher aboveground biomass production compared to the high-marsh genotype. Additionally, the low-marsh genotype generally formed longer rhizomes, shoots and leaves, regardless of flooding frequency. Belowground biomass of both genotypes decreased with increasing flooding frequency. We conclude that the low-marsh genotype is better adapted to higher flooding frequencies through its ability to allocate resources from below- to aboveground biomass. Given the strong control of plant biomass production on salt-marsh accretion, we argue that these findings yield important implications for our understanding of ecosystem resilience to SLR as well as plant species distribution in salt marshes.