Abstract: Microbial interactions in the phyllosphere have been shown to fulfil important functions for plant health. Yet, little is known about such types of microbial interactions in crop pathosystems and if they are influenced by host plant genotype. In this work, the endophytic and epiphytic fungal community in olive tree leaves with and without symptoms of olive leaf spot (OLS) disease, from three cultivars with different susceptibilities to OLS was compared. Fungal community was analysed by culture-dependent methods. Results indicate that fungal community differs in size and composition between asymptomatic and symptomatic leaf, especially within epiphytic community. Endophytes varied less probably due to enhanced complexity of interactions, since living host tissues were involved. Host genotype had a structuring effect on the composition of fungal communities only in asymptomatic leaves. Symptomatic leaves displayed a similar fungal community among cultivars, where composition appeared to be disease-specific. OLS disease also differentially influenced fungal flora of the three cultivars, and the greatest differences between asymptomatic and symptomatic leaves were observed in the tolerant cultivar. Some fungal taxa were found to be specific to either asymptomatic or symptomatic leaves, which suggested that they might have competitive or cooperative activity with the pathogen, within and outside leaf tissues. The role of these fungi as “pathogen antagonists” or “pathogen facilitators” must be investigated in the future.