Species delimitation in the genus Geopora (Pyronemataceae) is complicated because of small number of differentiating characters, values of which tend to overlap among the species. Current classification relies mainly on size and shape of ascospores and fruit-bodies, position of the apothecia in the ground and length of excipular hairs. We measured ascospores in ca. 90 Geopora specimens. Sequences of internal transcribed spacer (ITS) rDNA gene were obtained to investigate phylogenetic relationships in the genus. Maximum parsimony (MP) and Bayesian analyses reveal that the well-supported clades detected often do not correspond to the species concepts based on morphological characters. Nine out of the ten lineages include specimens which were initially identified as belonging to different species. The dimensions of ascospores vary to great extent within the lineages. The size and shape of fruit-bodies, length of excipular hair and hymenium colour are mostly homogenous within each clade; however, these characters coincide to a great extent among the lineages and the latter can be assessed only from fresh fruit-bodies. Nuclear DNA content, and accordingly, ploidy level do not provide evidence for species distinction. Geopora arenicola, G. tenuis and G. sepulta were recognized as monophyletic species. Geopora foliacea and G. cervina could not be explicitly delimited and the G. cervina complex comprising three clades was introduced.