Biodiversity loss in aquatic ecosystems is believed to have cascading effects on multiple trophic levels. In particular the phytoplankton-zooplankton interface is of high interest, as the phytoplankton content of dietary polyunsaturated fatty acids (PUFAs) was found to be crucial for the fitness of the herbivorous grazer Daphnia. However, fatty acid composition of the phytoplankton was shown to be taxon-specific. Thus, we hypothesized that altered phytoplankton community composition will result in an altered composition of dietary fatty acids. This in turn will affect the intraspecific competition in Daphnia. To address these hypotheses, we performed a common garden experiment with diversity-manipulated natural phytoplankton community and naturally coexisting D. longispina genotypes with pronounced differences in their performance in absence of essential PUFAs. Our data demonstrate that the phytoplankton diversity is correlated with the fatty acid composition, and that specific PUFAs directly affect competitive interactions between tested D. longispina genotypes.