The composition of the endophytes in a plant (i.e. organisms that live inside without causing any visible symptom) is gaining increasing attention in research as a functional part of the host plant, but the factors and processes shaping the composition of the these communities are still not well understood. In the present study, we evaluated whether the fungal endophytic community is shaped more strongly by the host species identity (substrate quality) or by the potential disturbance caused by co-occurrence of an aggressive pathogen in the network of microbial interactions. We focused on the diversity of fungal endophyte communities in five pine species (Pinus radiata, Pinus pinaster, Pinus sylvestris, Pinus nigra and Pinus uncinata) previously inoculated with the forest pathogen Fusarium circinatum and grown in a common environment. The results of our study revealed the existence of a core microbiome that was composed of nine operational taxonomic units (OTUs) and that was not dependend either on the host species or the presence of the pathogen. We foundinterspecific variation in the host of the fungal community composition and abundance. The co-occurrence of F. circinatum did not seem to influence the diversity of the fungal community although although some OTUs were unique indicators of presence of the pathogen. The results highlight the importance of host species as a determinant of microbiome assembly.