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Based on published anatomical-morphological and ecological characteristics and phylogenetic evidence, six species of the <i>Ganoderma</i> genus are known to occur in Europe, namely, <i>G. applanatum</i> (Pers.) Pat., <i>G. adspersum</i> (Schulzer) Donk, <i>G. pfeifferi</i> Bres., <i>G. resinaceum</i> Boud., <i>G. carnosum</i> Pat., and <i>G. lucidum</i> (Curtis) P. Karst. Molecular markers (DNA sequences of selected genes or intergenic spacers) revolutionized our view of fungal variability. Every one of the four most frequently used molecular markers (ITS (internal transcribed spacer) and partial sequences of LSU (rRNA large subunit), tef1-α (translation elongation factor 1-alpha), and Rpb2 (RNA polymerase II second largest subunit)) provides a different view on the variability of European species of the <i>Ganoderma</i> genus. Both the lowest intraspecies variability and the best species differentiation (interspecies divergence) were observed for the LSU marker, and based on our data, this marker could be recommended for identification and species delineation in European <i>Ganoderma</i> spp. The sequences of the most frequently used ITS marker were unable to discriminate between <i>G. lucidum</i> and <i>G. carnosum,</i> and in general, this species pair showed the lowest interspecies divergence using all markers tested. Surprisingly, up to now, hidden variability has been detected in several <i>Ganoderma</i> spp., indicating the existence of possible cryptic taxa within the European <i>Ganoderma</i> morphospecies.