The factors shaping the composition of microbial communities in trees remain poorly understood. We evaluated whether the core and satellite fungal communities in five pine species ( Pinus radiata, Pinus pinaster, Pinus sylvestris, Pinus nigra, and Pinus uncinata ) were shaped by the host species identity. Because the trees had earlier been inoculated with a fungal pathogen ( Fusarium circinatum ), we also explored the possibilities to detect its presence and potential co-occurrence networks. We found interspecific variation in the fungal community composition and abundance among the different tree species and the existence of a core microbiome that was independent of the host species. The presence of F. circinatum was confirmed in some samples through qPCR but the pathogen did not co-occur with a specific fungal community. The results highlight the importance of host species as a determinant of microbiome assembly in common environments.