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The presence of endophytic fungi in the roots, rhizomes, and leaves of <i>Posidonia oceanica</i> was evaluated in different localities of the Sicilian coast. Samples of roots, rhizomes, and leaves were submitted to isolation techniques, and the obtained fungal colonies were identified by morphological and molecular (rRNA sequencing) analysis. Fungal endophytes occurred mainly in roots and occasionally in rhizomes and leaves. <i>Lulwoana</i> sp. was the most frequent of the isolated taxa, suggesting a strong interaction with the host. In addition, eight other fungal taxa were isolated. In particular, fungi of the genus <i>Ochroconis</i> and family <i>Xylariaceae</i> were identified as endophytes in healthy plants at all sampling stations, whereas <i>Penicillium glabrum</i> was isolated at only one sampling station. Thus, several organs, especially roots of <i>Posidonia oceanica</i>, harbor endophytic fungi, potentially involved in supporting the living host as ascertained for terrestrial plants.