The fungal endophytic communities play an important ecological role in forest ecosystems. Many endophytic fungi are simple commensals, while others establish mutualistic relationships: the plant generally supplies nutrients and shield to the endophyte which, in turn, contributes with secondary metabolites to improve the host's vegetative condition. However, some fungi living in plant tissues may become opportunistic pathogens when their hosts grown under stress. These are particularly relevant in the pathogenesis of serious decline phenomena, which for over twenty years have been causing heavy blight to various forest species, especiallv Quercus spp., in Mediterranean countries. In this study, species diversity, distribution and abundance of endophytic fungi isolated from cork oak leaves and twigs in healthy and declining stands, were compared. The results show a varying assemblage of endophytic species in cork oak trees between healthy and declining stands, characterised by different environmental conditions. Over three years the lowest values of both soil moisture content and De Martonne aridity index were recor- ded in the declining stand. The highest similarities in endophyte canopy assemblages occurred among sites of the same stand. The fungal communities include few dominant species, among which Biscogniauxia mediterranea is the most frequent. Bionectria solani and Trichoderma fertile, endowed with antagonistic activities, were detected only in the healthy stand.