Hypolithic cyanobacterial communities occur in hot and cold hyperarid environments but the physical factors determining their diversity are not well understood. Here we report hypolithic diversity and colonization of a common quartz substrate at several hyperarid locations in the ancient deserts of north-western China, that experience varying mean annual temperature, rainfall and concomitant availability of liquid water in soil. Microscopy and enrichment culture resulted only in Chroococcidiopsis morphotypes which were ubiquitous, but community phylogenetic analysis revealed considerable cyanobacterial and heterotrophic bacterial diversity. Species Richness and Shannon's Diversity Index displayed a significant positive linear correlation with availability of liquid water but not temperature or rainfall alone. Several taxonomic groups occurred only in specific climatically defined locations, while for Chroococcidiopsis, Deinococcus and Phormidium location specific lineages within these genera were also evident. Multivariate analysis was used to illustrate pronounced community shifts due to liquid water availability, although these did not significantly affect the predicted functional relationships within any given assemblage in either hot or cold, wet or dry hyperarid deserts. This study clearly demonstrates that availability of liquid water, rather than temperature or rainfall per se is the key determinant of hypolithic diversity in hyperarid locations, and furthermore that functionally similar yet taxonomically distinct communities occur, characterized by the presence of taxa that are specific to defined levels of aridity.