Phylogenetic relationships among the hypothetical species pairs Lobaria kurokawae / L. retigera and L. pseudopulmonaria / L. isidiosa were investigated based on TLC techniques and the phylogenetic analysis of the internal transcribed spacers (ITS) nrDNA. Results of TLC demonstrate that L. retigera and L. kurokawae can be chemically distinguished from L. isidiosa and L. pseudopulmonaria by the absence of retigeranic acid. Parsimony analysis of 18 specimens shows two monophyletic clades – a L.retigera lineage and a L. isidiosa lineage—both including their apotheciate counterparts. Unlike the original hypothesis of species pairs, our study reveals transitions from isidiate morphs that have the potential to rarely form apothecia, towards apotheciate morphs that produce no vegetative propagules.