Lichen population genetics is a vastly under-studied field. The genus Sticta has been shown to contain species which are great bioindicators for air quality and the health of woodland habitats and accordingly has been included in recent governmental monitoring programs. Population structure data is an important component needed to inform decisions on conservation and forest health monitoring. This study focuses on Sticta canariensis, an easily identifiable foliose macrolichen that can form symbioses with either green algal or cyanobacterial photobionts. It has a limited range, mostly in Macaronesia, southwestern Norway, the United Kingdom, and Ireland. This, combined with its vulnerable status, makes S. canariensis a prime candidate for inclusion in conservation plans in these locations. However, there is little knowledge about its genetic diversity or population structure. In this study, we generated microsatellite data that informs about the genetic diversity of S. canariensis within the Macaronesian islands and in western Europe. The S. canariensis mycobiont forms genetically subdivided populations across disjunct habitats and there is limited gene flow among the island populations of Macaronesia. The data was consistent with ancient dispersal among distantly isolated habitats, with evidence for a few modern migration events. Funding: SW (DFG).