In the Atacama Desert, cyanobacteria grow on various substrates such as soils (edaphic) and quartz or granitoid stones (lithic). Both, edaphic and lithic cyanobacterial communities have been described but no comparison between both communities of the same locality has been undertaken there yet. In the present study we compared both cyanobacterial communities along a precipitation gradient ranging from the arid National Park Pan de Azúcar (PA) which resembles a large fog oasis in the Atacama Desert extending to the semi-arid Santa Gracia Natural Reserve (SG) further south, as well as along a precipitation gradient within PA. Various microscopic techniques as well as culturing and partial 16S rRNA sequencing were applied to identify 21 cyanobacterial species with a decrease in diversity with decreasing levels of precipitation. Also lithic cyanobacterial communities became more distinct compared to the surrounding edaphic community under increasing xeric stress, resulting in indigenous hypolithic and chasmoendolithic cyanobacterial communities. We conclude that, rain and fog water, respectively, are causing contrasting trends regarding cyanobacterial species richness in the edaphic and lithic micro-habitats.