The ectomycorrhizal fungi have a beneficial impact on plant growth and nutrient cycling in forest ecosystems. The differentiation of an effective symbiosis induces a series of complex and overlapping morphogenetic processes in the colonizing mycorrhizal hyphae and lateral roots of host trees. Up- and down-regulation of gene expression is a major mechanism for controlling ectomycorrhizal symbiosis development and functioning. Transcript profiling studies led to the identification of genes that are required for fungal attachment, plant defense, and symbiosis-related metabolism. They showed that changes in morphology associated with mycorrhizal development were accompanied by alteration in transcript patterns. Comparison of the genomes of the different pathogenic and saprobic fungi with the ectomycorrhizal Laccaria bicolor genome revealed that the symbiont genome encodes several features found in saprotrophic and biotrophic fungi, but it lacks the extensive set of cell wall hydrolytic enzymes encoded by soil white-rot fungi and necrotrophic phytopathogens. Genome-wide studies are providing crucial insights into the genetic makeup of mycorrhizal interactions.