Sticta canariensis is a lichen which is rare in all parts of its range in Atlantic Europe and Macaronesia, where it occurs in laurisilva forests, a habitat highly threatened by global change. Thus, this species is of high priority for inclusion in conservation programmes where genetic diversity should be considered. We have established new microsatellite loci and generated a dataset that demonstrates the genetic diversity of the lichen-forming fungus S. canariensis from eight locations across its disjunct range, in Macaronesia, Norway and England. We genotyped 25 microsatellite loci for 65 specimens and detected five genetic clusters which resemble major geographical divisions, specifically among the Macaronesian archipelagos. The total number of observed alleles ranged from 2 to 22. These are the first microsatellite markers developed for S. canariensis and they will be useful for population genetic studies and for conservation assessments. England, Macaronesia, Norway, Peltigeraceae, genetic diversity, population structure