Pleistocene erratic boulders sometimes harbour exclusive rock-dwelling cryptogams (bryophytes, ferns and lichens) and thereby contribute to the biodiversity of landscapes. This is especially the case where erratic boulders constitute the only natural rock habitats or where the chemical composition of boulders contrasts with surrounding bedrock composition. In the calcareous Swiss Plateau and Jura Mountains, about 27 bryophyte, one fern and numerous lichen species exclusively occur on siliceous erratic boulders. Despite their significance for biodiversity, glacial history and island biogeography, conservation aspects of cryptogams on Swiss siliceous erratic boulders have never been considered. Moreover, these spatially isolated communities face threats such as land use changes and rock climbing (bouldering). The present study thus aims at creating the scientific foundations for the conservation of cryptogam communities on siliceous erratic boulders. Current bryophyte and vascular plant diversities and their main ecological determinators will be analysed with general linear models in six to eight study regions with 20 to 40 siliceous erratic boulders per region. The effect of chalk used in climbing and bouldering on calcifuge rockdwelling bryophytes and ferns will be assessed in full factorial experiments in climate chambers. Conservation relevant population processes will be addressed in the fern Asplenium septentrionale and the moss Hedwigia ciliata based on single nucleotide polymorphisms (SNP) retrieved from double digest restriction associated DNA sequencing (ddRAD). The studies’ outcomes will allow developing conservation measures for cryptogam communities on erratic boulders as well as for isolated populations of rockdwelling cryptogams in general.