The structure of ectomycorrhizal communities was assessed above- and below-ground at three different sites in Switzerland that are dominated by Norway spruce (Picea abies (L.) Karst.). We applied three different approaches to record the ectomycorrhizal species compositions and their spatial structures and compared them among each other. Sporocarp inventories were carried out weekly for 3 years. Belowground, molecular, and morphological analyses of ectomycorrhizal roots were performed. In the 3 years of sporocarp survey, a total of 128 ectomycorrhizal species was observed. Most abundant in number of species were the genera Cortinarius and Russula in all three sites. Using polymerase chain reaction, only 22% of the ectomycorrhizal species observed in sporocarp surveys were detected in mycorrhizas. Species that produce no or inconspicuous sporocarps were most abundant on the root system in all three study sites. The resolution was clearly inferior in morphotype compared with molecular analyses. Spatial analyses of the ectomycorrhizal species composition among subplots revealed high variability within sites. Within sites, spatial structure with positive autocorrelation was observed based on sporocarp data as well as molecular analyses of root tips at the site where the number of analysed mycorrhizas was sufficiently high. No spatial structure could be detected on this scale by morphotype analyses because of the high variability among soil cores. All three methods showed the same site to be separated from the other two based on ectomycorrhizal species compositions. Stand ages and their histories are discussed as possible explanations for these findings