Several morphological species of the genus Hydnum L. are known to occur in Europe, but little molecular evidence exists to confirm the exact number and delimitation of the species. The present study seeks to investigate the genus Hydnum through sequence analysis of the nuclear ribosomal ITS regions and through morphological studies. The DNA sequences phylogenetic analysis revealed high diversity among the ITS region sequences in H. repandum (two clades) and H. rufescens (six clades) while the specimens of H. albidum, H. umbilicatum and H. ellipsosporum formed one and clearly separated clade per morphological species. Phylogenetic distances among the recognised species and the obtained morphologically unsupported clades are comparable and support the idea of several new, yet undescribed species. The intraspecific variability in the sequence data among phylogenetic species is generally low. Detailed morphological analysis of putative informative morphological characteristics could not support any of the observed non-monophyletic DNA-sequences clades within H. repandum or H. rufescens, and the proper use of names is not yet clear. Similar intraspecific variation has also been observed in many other ectomycorrhizal genera and could be explained by intensive speciation within variable groups under the influence of various factors (niche effect, ectomycorrhizal partner selection).