The specific interactions of fungi with plants include the mutually beneficial mycorrhizal symbioses and an increasing number of case studies, where endophytic fungi communicate with their host plant to allow for beneficial interactions. The omics methods development has allowed for a substantial increase in knowledge that emphasized in many cases the intricate interplay between the symbiotic partners. In addition to the direct interactions, the mycorrhizosphere comes into view, as the fungal soil mycelium is interacting with the community outside the host plant, transferring signals also to the host. This Research Topic encompasses research on both major types of mycorrhizal interactions, endo- and ectomycorrhiza, and includes communication with the environment in which both partners interact with soil microbes. The mycorrhizosphere is in the center of molecular biology and modern ecological research, greatly fostered by the possibilities of genetic manipulation.