Olive tree phyllosphere is colonized by a diverse microbial assemblage that may interact with pathogenic fungi, making them potential candidates for disease supression. Olive knot (OK) is a disease caused by the bacterium Pseudomonas savastanoi pv. savastanoi (Psv.) with significant economic losses in olive tree (Olea europaea L.). With this work we want to evaluate the effect of cultivar and OK infection on both endo- and epiphytic fungal community inhabiting olive twig tissues. For this, fungal composition and diversity was assessed in both asymptomatic and OK-symptomatic twigs of tree co-occurring olive cultivars with different susceptibilities to OK disease. The identification of isolated species was performed by ITS rDNA sequencing. The cultivar and OK infection were important in shaping both endophytic and epiphytic fungal communities. Fungal community composition was found to differ significantly (p=0.005) between olive tree cultivars, being Nectriaceae the dominant family in cvs. Cobrançosa and Verdeal Transmontana, whereas Pleosporaceae was dominant in the cv. Madural. Epiphytic and endophytic fungal communities also differed in size and in composition in asymptomatic and OK-symptomatic twigs, for the three cultivars. In general, asymptomatic twigs were more diverse and rich (up to 1.4-fold) when compared to OK-symptomatic twigs. Among the species identified in the asymptomatic tissues, Cladosporium cladosporioides and Chromelosporium carneum were the most frequently isolated within epiphytic and endophytic community, respectively; whereas in the OK-symptomatic tissues Cladosporium sp. and Fusarium lateritium were the most frequently isolated within epiphytic and endophytic community, respectively. According to indicator species analysis C. carneum, Pyronema dosmesticum and Phoma aloes (IndVal up to 0.56) may be promising species in the OK suppression. Better acknowledgement should be developed in order to uncover their role on plant health.