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This study explores the diversity of photobionts associated with the Mediterranean lichen-forming fungus <i>Cladonia subturgida</i>. For this purpose, we sequenced the whole ITS rDNA region by Sanger using a metabarcoding method for ITS2. A total of 41 specimens from Greece, Italy, France, Portugal, and Spain were studied. Additionally, two specimens from Spain were used to generate four cultures. Our molecular studies showed that the genus <i>Myrmecia</i> is the main photobiont of <i>C. subturgida</i> throughout its geographic distribution. This result contrasts with previous studies, which indicated that the main photobiont for most <i>Cladonia</i> species is <i>Asterochloris</i>. The identity of <i>Myrmecia</i> was also confirmed by ultrastructural studies of photobionts within the lichen thalli and cultures. Photobiont cells showed a parietal chloroplast lacking a pyrenoid, which characterizes the species in this genus. Phylogenetic analyses indicate hidden diversity within this genus. The results of amplicon sequencing showed the presence of multiple ASVs in 58.3% of the specimens studied.