Extreme climatic events can lead to rapid yet long-term ecosystem alteration, especially when such events impact foundation species. The response and recovery of these foundation species will depend on the diversity and plasticity of traits within these species. However, it is often unknown which traits determine foundation species’ performance under average compared to extreme climatic conditions. Eelgrass Zostera marina is a marine foundation species distributed along coastlines throughout the northern hemisphere, on which a unique community of fishes and invertebrates depends. We assessed the performance (i.e. productivity) of 36 genotypes of Z. marina across winter and summer seasons, during one average year (2013) and one year in which summertime temperatures were 2.5°C above average (2014). We used structural equation modeling to relate trait data to variation in performance of genotypes across environmental conditions. Genotypes with the highest productivity during winter were predicted by traits related to light capture (leaf length and photosynthetic efficiency). During the extremely warm summer, genotypes with the lowest winter shoot densities, the longest summer leaves, and the lowest sensitivity to high light (least photoinhibited) achieved the highest productivity. Because traits related to high winter performance differed from traits related to high summer performance, genotype performance rank order shifted through time. By directly linking functional trait differences to performance, our results demonstrate how genotypic composition could be shifted by an extreme climatic event and how genetic diversity may contribute to population resilience in the face of a changing climate.