Ectomycorrhiza formation is a complex developmental process that is still not well understood. To study this process, we identified genetic markers for mycorrhiza development by differential screening of a cDNA library obtained from fully developed Picea abies–Amanita muscaria mycorrhizas. Twenty-three cDNA clones were identified that showed significantly altered gene expression during the ectomycorrhizal interaction. A detailed analysis was performed for two fungal cDNA clones, SC13 and SC25, exhibiting the most pronounced differences. SC13 encodes a protein of 184 amino acid residues that shows no homology with any sequence in databases. It was highly expressed in non-mycorrhizal hyphae, whereas its expression was decreased at least 50-fold in mycorrhizas and fruit bodies. SC25 encodes a protein of 198 residues that shows weak sequence homology with extensin-like plant proteins. The expression of this gene was weak in non-mycorrhizal hyphae but approx. 30-fold higher in mycorrhizas and fruit bodies. Because the expression of both developmentally regulated fungal genes was identical for mycorrhizas and fruit bodies, a common regulation mechanism for both developmental processes is proposed.