The ectomycorrhiza formation involves intense gene expression control in both partners that leads to several morphological and physiological changes. The purpose of this chapter was to review the main genes from ectomycorrhizal fungi (EMF) expressed in association with roots or under mycorrhizal stimulus. Researchers looked at different EMF and host interactions, and screened different experimental conditions and techniques. It was possible to group a large number of ectomycorrhizal genes/proteins into different physiological categories according to probable functions within symbiotic associations. In total 389 ESTs/proteins were listed from different fungal genus and species. Ectomycorrhizal genes were grouped in eight physiological categories as follows (1) cell growth and organization, (2) morphogenesis, (3) energy metabolism, (4) protein synthesis and protein interaction, transcriptional and translation regulation, (5) ion transport, amino acid and peptide transport, (6) cell signaling and structural membrane proteins, (7) RNA/DNA processing and (8) cell defense and apoptosis. We observed that related genes change their expression level during formation and maintenance of symbiotic relationships; however, all of them are basally expressed in most symbiotic conditions. There seems to be a tendency for gene expression suppression (down-regulation) during short association periods or even during the preinfection interaction. This tendency can be observed in protein synthesis genes, carbon metabolism genes and membrane proteins like SRAPs and hydrophobins, which are proteins believed to be important agents for ectomycorrhiza formation. However, genes of unknown function can highlight a knowledge gap concerning fungal origin sequences in symbiosis, and alert the urgent need to encourage future studies in molecular ectomycorrhizal associations.