Hypolithic microbial communities are specialized desert communities inhabiting the underside of translucent rocks where they are sheltered from harsh environmental conditions. Here, we present the first study of the viral fraction of these communities isolated from the hyperarid Namib Desert (coastal South Western Africa). Using next-generation sequencing of the isolated viral fraction, the diversity and taxonomic composition of hypolith communities was mapped and a functional assessment of the sequences determined. Phylotypic analysis showed that bacteriophages belonging to the order Caudovirales with the family Siphoviridae were most prevalent. A major fraction of phage types was linked by database homologies to Bacillus or Geobacillus sp. as a host. Phylogenetic analyses of terL and phoH marker genes indicated that many of the sequences were novel and distinct from known isolates and environments, an observation supported by the class distribution of identified ribonucleotide reductases. The composition of the viral hypolith fraction was not completely consistent with Namib hypolith phylotypic surveys, in which the cyanobacterial genus Chroococcidiopsis was found to be dominant. This could be attributed to lacking sequence information about hypolith viruses/bacteria in public databases or the hypothesis that hypolithic communities actively recruit viruses from the surrounding open soil in which Bacillaceae-infecting phages are more commonly found.