Lichens are present in most terrestrial ecosystems on Earth and colonize extreme habitats, where vascular plants are unable to thrive, due to unique properties of the fungal-algal symbiosis. Here, we explored the phylogeographic structure of green algae engaged in symbiosis with species in the genus Pseudephebe (Parmeliaceae). These often form deep brown to blackish fruticose thalli on acidic rocks, and have partially overlapping distributions: P. minuscula is bipolar and co-occurs with P. pubescens in Europe. Based on a broad sampling, including the Arctic and Antarctica, we focused on photobionts (1) to identify genetic lineages and their phylogenetic assignment, (2) to infer the haplotype distribution in relation with geography and the mycobiont's identity, and (3) to evaluate spatial genetic structure and polymorphism. Results revealed three Trebouxia clade S lineages (Trebouxia S02, T. suecica and T. angustilobata) associated to Pseudephebe species, with predominant haplotypes distributed throughout the entire geographic distribution, and some, less frequent, shared between widely distant localities. Photobiont switching was evident in the Mediterranean region, and algal co-occurrence was frequent in both mycobionts, which shared the same set of photobionts; this could explain, at least partially, their overlapping distribution. Furthermore, genetic structure was influenced by geography given the substantial percentages of genetic variation (ca. 25-50%) explained by the different delimited eco−/biogeographic regions. In Continental Antarctica, mycobionts showed a high specialization towards the photobionts, which are probably endemic of this climatically extreme region. Taken together, our findings provide further insight about the processes shaping lichen biogeography.