Species delimitation is still controversial in the Xerocomus chrysenteron complex. We have therefore established comprehensible and reliable species concepts based on statistical evaluation of morphological and ecological characters. We examined many collections from different geographical regions and different developmental stages within collections. Quantitative micromorphological characters (basidiospores, pileipellis end cells) were measured in statistically relevant numbers. The same material was used to generate 24 rDNA-LSU sequences, and the results of phylogenetic analyses clearly confirmed our species concepts: spore size and ornamentation, length of the pileipellis end cells and ‘pruinatus-hyphae’ are most valuable characters for the delimitation of species in this complex. Molecular data demonstrated that the X. chrysenteron complex is a monophyletic group. All the examined species (X. chrysenteron, X. cisalpinus, X. pruinatus, X. ripariellus, X. dryophilus, X. fennicus, X. porosporus, and X. rubellus) represent independent lineages. The faintly striate spores, a key character characterising species of section Striatulispori, probably evolved independently. In addition, the ‘pruinatus-hyphae’ have multiple origins, and truncate spore apices are derived at least twice. Xerocomus cisalpinus sp. nov. is characterised by striate spores, the presence of ‘pruinatus-hyphae’ and a pileipellis strongly reminiscent of X. chrysenteron. For reasons of discussion, microscopical data are presented on Boletellus episcopalis for the first time. Xerocomus fennicus (Boletellus) comb. nov. is proposed. We provide descriptions to all included taxa. Our results once more demonstrate that reliably identified and characterised voucher collections are the basic requirement for meaningful phylogenetic studies.