Stereocaulon alpinum is a lichenized fungus commonly found in the Antarctic, circumarctic, alpine, and in mountainous areas of temperate regions. It forms a tripartite lichen symbiosis together with trebouxioid green microalgae, as its primary photobiont, and cyanobacteria of the genus Nostoc inside delimited cephalodia. Previous DNA-based analyses revealed two lineages for this fungus. This research discusses the morphological and chemical circumscription of S. alpinum and its geographic distribution and, to this end, we included new DNA data from the mycobiont and its photosynthetic partners. Phylogenetic reconstructions rejected infraspecific categories and revealed that specimens from the southern hemisphere (maritime Antarctica and South America) formed a well-supported “bipolar clade” with specimens from Finland, Greenland, and Canada. In addition, S. alpinum also formed a “northern clade” with sequences from Europe and North Atlantic islands. In specimens from the southern hemisphere, the identified lineages of phyco- and cyanobionts were already known to be associated with other lichenized fungi. The phycobiont was identified as Asterochloris pseudoirregularis and the cyanobiont as a member of the genus Nostoc. The phenotypic differences among the southern hemisphere specimens examined in this study pointed towards a broad morphological circumscription of S. alpinum. Simultaneously, the available descriptions of S. alpinum collected in the northern hemisphere, including the type specimen, do not provide characters distinguishing them from the southern specimens. These two clades likely represent cryptic species, one new and potentially only recognized using genetic data. Additional integrative studies, including a comprehensive analysis of specimens from the northern hemisphere, are necessary to know the diversity contained in the lichens identified as Stereocaulon alpinum worldwide.