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Although rocks are habitable places for microbes in extreme environments, microbial diversity in these lithic environments is still poorly understood. The diversity and abundance of rock-inhabiting microbial communities in different types of rock in Svalbard, Norwegian High Arctic were examined using NGS sequencing of bacterial 16S rRNA genes and fungal 28S rRNA genes. Compositions of both bacterial and fungal communities varied across different rock types: sandstone, limestone, basalt, granite and travertine. Bacterial communities were dominated by Actinobacteria, Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. Fungal communities consisted of Eurotiomycetes, Lecanoromycetes, Dothideomycetes and Leotiomycetes. Both bacterial and fungal community compositions were significantly correlated with the geochemical characteristics of rocks. Bacterial communities were considerably correlated with the rock elements such as Mg and Ca. Fungal communities were considerably correlated with Fe. Interestingly, many dominant bacterial and fungal operational taxonomic units in the investigated rocks from the study area were closely affiliated to those found in other cold regions such as Alpine area, Arctic and Antarctica, suggesting that environmental constraints such as cold temperature may lead to convergence in microbial community composition. These results confirm that rocks in cold environments act as reservoirs of diverse bacteria and fungi, which may improve our understanding of lithic microbial ecology in the cold desert.