Extensive morphological and molecular analyses of closely related species from alpine, subalpine and montane habitats should enable a comparison of ecological, morphological and phylogenetic species concepts in ectomycorrhizal mushrooms. One fundamental question of this study was whether alpine species really exist, and which criteria, besides the specific habitat, could reliably be used for the de-limitation of such taxa. For this reason, 56 rDNA ITS sequences were generated or downloaded from GenBank for 10 closely related species of Cortinarius subgenus Myxacium, section Myxacium. Several collections were sequenced for each of the following taxa: Cortinarius absarokensis, C. alpinus, C. favrei, C. fennoscandicus, C. grallipes, C. mucosus, C. muscigenus, C. septentrionalis, C. trivialis and C. vernicosus. Moreover, spore statistics were carried out for 38 collections of alpine and subalpine taxa. These data provide clear evidence for C. favrei being a synonym of C. alpinus. C. absarokensis and C. alpinus can clearly be delimited based on pileus diameter and average dry weight per basidiome, even in overlapping habitats, but spore size and shape is not a good distinguishing character. Phylograms have very short branches, and base differences between ITS sequences are generally very low in this group, and give no resolution for the included taxa of this section. Based on these results, species concepts of ectomycorrhizal mushrooms are discussed in detail.