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Isolation and patchiness are the most prominent features of Antarctic terrestrial biota. The geographic isolation from other continents and restriction to widely scattered and small habitat patches have led to high levels of endemism and strong bioregionalisation. This has created opportunities for genetic differentiation, local adaptation and the evolution of cryptic lineages. Lichens are symbiotic associations consisting of a fungal (mycobiont) and one or more photosynthetic partners (photobionts) and are the dominant component and most important primary producers of Antarctic terrestrial ecosystems. In spite of their ecological importance, there is almost no data on the genetic structure and diversity of Antarctic lichen populations. Levels of inter- and intracontinental gene flow are entirely unknown to date. Lichens have developed reproductive strategies that involve both sexual and asexual propagules. Based on short tandem repeats (microsatellites) we investigate the population structure of four lichens with different propagation strategies. We sampled and genotyped populations of Usnea aurantiacoatra and U. antarctica, Placopsis contortuplicata and P. antarctica from several areas of the northern Antarctic Peninsula and southern South America to better understand the genetic variability und structure of their populations and infer possible gene flow between the two continents. [ABSTRACT FROM AUTHOR]