In this study we examined the microbial community composition developed on three different silicate minerals (muscovite, feldspar and quartz) sampled from three spatially separate domains along a sub-vertical 10 metre long pegmatitic granite outcrop. We investigated the influence of mineral type on bacterial and fungal community structure. A DNA-based community fingerprinting approach (ARISA—automated ribosomal intergenic spacer analysis) was used to assess the nature and extent of microbial diversity. The molecular biology approach was combined with multivariate statistics: canonical analysis of principal coordinates (CAP) and permutational multivariate analysis of variance (PERMANOVA) to identify the main geochemical factors that influence microbial community structure in situ. We found that bacterial and fungal community structure was strongly influenced by the chemistry of the silicate mineral, with many bacterial and fungal ribotypes limited to a single mineral type, and to a much lesser extent by the sampling location along the outcrop. The novelty of our findings is that mineral type exerted a very strong selection on bacterial and fungal community structure on the length scales ranging from a few centimetres to several metres. A number of 49 bacterial and 45 fungal strains were isolated from the studied mineral surfaces. Several archaea clones belonging to Crenarchaeota phylum were retrieved from the mineral samples and soil.