Genetic variation in a foundation species may affect the composition of associated communities as well as modify ecosystem function. While the ecological consequences ofgenetic diversity of foundation species have been widely reported, the ability of individualgenotypes to support dissimilar communities has been documented only in forest ecosystems.Here, for the first time in a marine ecosystem, we test whether the different genotypes of therockweed Fucus vesiculosus harbor distinct community phenotypes and whether the geneticsimilarity of individual genotypes or their defensive compound content can explain the variation of the associated communities. We reared replicated genotypes in a common garden in thesea and analyzed their associated communities of periphytic algae and invertebrates as well asdetermined their contents of defense compounds, phlorotannins, and genetic distance based onneutral molecular markers. The periphytic community was abundant in mid-summer and itsbiovolume, diversity and community composition varied among the rockweed genotypes. Thediversity of the periphytic community decreased with its increasing biovolume. In autumn,when grazers were abundant, periphytic community biomass was lower and less variableamong rockweed genotypes, indicating different relative importance of bottom-up regulationthrough heritable variation of the foundation species and top-down regulation through grazingintensity. Similarly, composition of the invertebrate community varied among the rockweedgenotypes. Although the genotype explained about 10–18% of the variation in associated com-munities, the variation was explained neither by the genetic distance nor the phlorotannin con-tent. Thus, neither neutral genetic markers nor a single phenotypic trait could provide amechanistic understanding of the genetic basis of community specificity. Therefore, a morecomprehensive mapping of quantitative trait variation is needed to understand the underlyingmechanisms. The community specificity implies that genetic variation within a foundation spe-cies is crucial for the biodiversity and assembly of associated organisms and, thus, for the func-tioning of associated communities. The result highlights the importance of ensuring the geneticvariation of foundation species as a conservation target.