Basidiolichens are generally poorly researched because of the very small number of species and their restriction to special niches. Lichenomphalia basidiolichens grow in considerable quantities in arctic and alpine habitats but they are inadequately studied in these habitats in Mediterranean areas. Based on morphological and phylogenetic analyses, we identified the different symbionts of L. meridionalis, collected in localities in Spain at altitudes ranging from 533 to 2200 m above sea level. The present study provides the first molecular data available for L. meridionalis. We found that a microindel of six bp within the nrITS2 could help to discriminate L. meridionalis from other species of the genus. Molecular analyses revealed the existence of two different green algal strains, both belonging to Coccomyxa subellipsoidea, a species shared with other Lichenomphalia lichens. Notably, the two chlorobiont strains associated with L. meridionalis were differentially distributed according to altitude, and samples having one of the two strains consistently also included cyanobacteria.