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Erratic boulders provide habitat for rock-dwelling species and contribute to the biodiversity of landscapes. In the calcareous Swiss lowlands, siliceous erratic boulders are exclusive habitat islands for the regionally critically endangered fern  Asplenium septentrionale , about 20 bryophyte species and numerous lichens. Focusing on island biogeographical processes, we analysed the conservation genomics of  A. septentrionale  and the moss  Hedwigia ciliata  on insular erratic boulders in the Swiss lowlands and the adjacent “mainland” in siliceous mountains. We genotyped both species using double digest restriction associated DNA sequencing (ddRAD). For the tetraploid  A. septentrionale , abundant identical multilocus genotypes within populations suggested prevalent intragametophytic selfing, and six out of eight boulder populations consisting of a single multilocus genotype each indicated single spore founder events. The genetic structure of  A. septentrionale  mainland populations coincided with Pleistocene glacial refugia. Four genetic lineages of  H. ciliata  were identified, and populations consisting of a single multilocus genotype were less common than in  A. septentrionale . For both taxa, multilocus genotype diversity on boulders was lower than in mainland populations. The absence of common genetic groups among boulder populations, and the absence of isolation by distance patterns, suggested colonisation of boulders through independent long-distance dispersal events. Successful boulder colonisation of  A. septentrionale  seems to be rare, while colonisation by  H. ciliata  appears to be more frequent. We conclude that pivotal principles of conservation biology, such as connectivity and genetic diversity, are of less importance for the studied cryptogams on insular erratic boulders because of long-distance dispersal, intragametophytic selfing and polyploidy.

Neither connectivity nor genetic diversity matter in the conservation of a rare fern and a moss on insular erratic boulders