Genetic diversity, like species diversity, can have important consequences for communities and ecosystems. However, little is known about whether the effects of genetic diversity demonstrated in experimental assemblages are of sufficient strength to generate patterns in natural systems. We conducted a survey of eelgrass (Zostera marina) to examine the correlation between eelgrass clonal diversity and two metrics of community structure across two seasons: shoot density (reflective of habitat quality) and biomass of epiphytic algae (as a measure of food resource availability). Eelgrass clonal diversity was not related to epiphyte biomass in either winter or summer. Interestingly, there was a positive relationship between eelgrass clonal diversity and shoot density only in the winter, when eelgrass experiences stress from abiotic and biotic factors. The magnitude of this correlation was similar to that of other factors known to affect shoot density such as tidal elevation or position in the bed. In contrast, summer shoot density and diversity were uncorrelated. This natural pattern is consistent with previous experimental results in which diversity positively affected shoot density only during periods of abiotic or biotic stress, suggesting that the effects of clonal diversity are sufficiently strong to influence shoot density in the field, despite the presence of potentially confounding environmental gradients.