The Integrated Ocean Drilling Program (IODP) Hole 1301A on the eastern flank of Juan de Fuca Ridge (JFR) was used as a long term sub-seafloor microbial observatory to determine microbial colonization preferences for twelve silicate minerals and glasses common in igneous rocks. Previous work revealed significant differences in total cell densities, with iron-bearing olivine minerals maintaining the highest densities of total cells, culturable organotrophic mesophiles, and the only culturable organotrophic thermophiles. Since 90% of identified culturable strains were able to oxidize iron in the laboratory, we hypothesized that iron-bearing minerals would support distinct communities from iron-poor minerals. Since most organisms are unculturable, inferences about differences in complexity between microbial communities colonizing minerals could best be made using high-throughput sequencing. We proposed to use 454 pyrosequencing and sequence analysis of the hypervariable V4 region of the SSU rRNA gene for bacteria and archaea using genomic DNA extracted from our mineral samples to test our hypothesis. Through this work, we found that mineralogy of the crust governed attached community assemblages, diversity, and distribution in deep ocean crust. We discovered that the olivine group of minerals had communities that were unique among igneous minerals and that they were the most diverse. Communities from iron-bearing minerals were more similar to each other than communities from iron-poor minerals, indicating there is an iron-related compositional influence on community development. We compared mineral communities to surrounding aquifer fluid and bottom seawater and found that attached communities differed considerably from their free-living counterparts. Our hypothesis was validated through this work, and the results have significantly increased our understanding of how mineralogy controls micro-scale diversity within igneous rocks. This work has allowed us a glimpse into ecosystem function in the largest habitat on Earth, and will allow us to better model reactive transport, weathering, and biogeochemical cycling in the ocean crust.