With rare exceptions, the shape and appearance of lichen thalli are determined by thefungal partner; thus, mycobiont identity is normally used for lichen identification. However, it hasrepeatedly been shown in recent decades that phenotypic data often does not correspond with fungalgene evolution. Here, we report such a case in a three-species complex of red-fruited Cladonia lichens,two of which clearly differ morphologically, chemically, ecologically and in distribution range. Weanalysed 64 specimens of C. bellidiflora, C. polydactyla and C. umbricola, mainly collected in Europe,using five variable mycobiont-specific and two photobiont-specific molecular markers. All mycobiontmarkers exhibited very low variability and failed to separate the species. In comparison, photobiontidentity corresponded better with lichen phenotype and separated esorediate C. bellidiflora from thetwo sorediate taxa. These results can be interpreted either as an unusual case of lichen photomorphsor as an example of recent speciation, in which phenotypic differentiation precedes the separation ofthe molecular markers. We hypothesise that association with different photobionts, which is probablyrelated to habitat differentiation, may have triggered speciation in the mycobiont species.