Ecological studies often assume that genetically similar individuals will be more simi-lar in phenotypic traits, such that genetic diversity can serve as a proxy for trait di-versity. Here, we explicitly test the relationship between genetic relatedness and trait distance using 40 eelgrass (Zostera marina) genotypes from five sites within Bodega Harbor, CA. We measured traits related to nutrient uptake, morphology, bio-mass and growth, photosynthesis, and chemical deterrents for all genotypes. We used these trait measurements to calculate a multivariate pairwise trait distance for all possible genotype combinations. We then estimated pairwise relatedness from 11 microsatellite markers. We found significant trait variation among genotypes for nearly every measured trait; however, there was no evidence of a significant correla-tion between pairwise genetic relatedness and multivariate trait distance among in-dividuals. However, at the subpopulation level (sites within a harbor), genetic (FST) and trait differentiation were positively correlated. Our work suggests that pairwise relatedness estimated from neutral marker loci is a poor proxy for trait differentia-tion between individual genotypes. It remains to be seen whether genomewide measures of genetic differentiation or easily measured “master” traits (like body size) might provide good predictions of overall trait differentiation