Plant landscape ecology studies have been carried out for decades and are fundamental to biological research. In contrast, few corollary spatial landscape studies exist for microorganisms, particularly in extreme environments. To address this gap, we mapped the abundance and spatial distribution of photoautotrophs colonizing translucent rocks in several sites in the Atacama Desert, including the hyperarid core. Cyanobacterial communities at all sites are predominantly (≥75%) ‘perilithic’ (confined to the periphery of rocks) and occur in non-random spatial patterns (“island patches”) at multiple scales. Cyanobacterial patches typically contain 1-5 colonized rocks but in some cases support much higher numbers. A high resolution mapping of a single 18-m2 rock cluster at the Aguas Calientes study site (25°S, 69°W) revealed colonization of 5.2% (49 of 948 quartz rocks) and showed colonized rocks to be much larger (∼2X) than the available mean rock size. Ripley's K and point pattern analyses show that quartz rocks are not “selected” or occupied by cyanobacteria randomly, but that non-random processes distinct from those creating the background rock pattern must be invoked to explain microbial patchiness in the Atacama Desert. These processes include physical controls (rock size/orientation, microtopography) that reflect resource (water) limitations, and biological dispersal via rainfall, fog and wind.