The Antarctic–South American bank-forming moss Chorisodontium aciphyllum is known for having the oldest sub-fossils of any extant plant in Antarctica as well as extreme survival abilities, making it a candidate species for possible long-term survival in Antarctica. Applying phylogeographic and population genetic methods using the plastid markers trnL-F and rps4 and the nuclear internal transcribed spacer, we investigated the genetic diversity within C. aciphyllum throughout its range. Low genetic variation was found in all loci, both between and within Antarctic and southern South American populations, suggesting a relatively recent (likely within the last million years) colonization of this moss to the Antarctic, as well as a likely severe bottleneck during Pleistocene glaciations in southern South America. We also performed a simple atmospheric transfer modeling approach to study potential colonization rates of small (microscopic/microbial) or spore-dispersed organisms (such as many mosses and lichens). These suggested that the northern Antarctic Peninsula shows potentially regular connectivity from southern South America, with air masses transferring, particularly southbound, between the two regions. We found elevated genetic variation of C. aciphyllum in Elephant Island, also the location of the oldest known moss banks (> 5500 years), suggesting this location to be a genetic hotspot for this species in the Antarctic.