Stigomena is a genus of cyanobacteria that is often the photobiont associated with the lichen genus Stereocaulon. To elucidate the evolutionary relationships between Stereocaulon and Stigonema and assess whether there is specificity or selectivity at the ecosystem or species levels, we performed phylogenetic analyses on specimens collected throughout Eastern Canada. We generated ITS sequences from the fungal component of the symbiosis and sequences from the operon rbcL-rbcX and the trnL intron from the cyanobacteria of seventy specimens of Stereocaulon. Our ITS results revealed that at least forty Stereocaulon specimens are in 16 distinct species clades (OTUs) and morphologically defined species tend to be paraphyletic. In addition, two genera of cyanobacteria, Stigonema and Nostoc, were detected among the samples and the former is the most common symbiont associated with Stereocaulon. We discovered that nearly invariable Stigonema sequences (rbcL-rbcX) occur across 2,000 km of sampling from temperate to arctic biomes. The lack of geographic structure or species-level specificity for Stigonema suggest a high co-dispersal capability of the cyanobacteria with the ascomycete and selectivity towards a small number of very similar Stigonema haplotypes across eastern Canada.