Antimicrobial resistance is a major global concern affecting public health. In this context, natural products (NPs) represent a reservoir of unique chemical scaffolds with potential antimicrobial properties. At present, the majority of naturally originated antibiotics have been isolated from soil microorganisms. Thus, investigation of NPs from marine endophytic strains in this regard is an expanding field. This thesis is within the frame of SECIL, a collaborative project between different research units in Switzerland and France which aims to perform a comprehensive study of the endophytic communities within model plants. In the present work, we investigated in particular the fungal endophytes within the tissues of the seagrass Posidonia oceanica. The main goal was to search for bioactive agents and to report new chemical entities biosynthesized by those endophytes. In total, 53 fungal metabolites from 6 selected strains were fully identified and their bioactive potential was evaluated.