Twenty-five microbial communities were sampled from 18 different hydrothermal systems located at seven different sites along the Mariana Island Arc and at a single site from the southern Mariana Spreading Center over a 3-year period. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the small subunit rRNA gene revealed that the microbial community diversity is much greater along the Mariana Arc/back-arc than at either hot spot volcanoes or mid-ocean ridges along the same spatial scale. Cluster analysis of T-RFLP fingerprints reveals the microbial communities formed three distinct clusters designated Mariana clusters I, II, and III. Microbial communities in Mariana Cluster I are all associated with iron-rich microbial mats and are dominated by members of the ζ-Proteobacteria and by unique phylotypes clustering deeply in the δ-Proteobacteria and within the Nitrospira division. Mariana Cluster II communities are all from shallow hydrothermal systems and mostly from colder sediments or microbial mats that are dominated by putative heterotrophic phylotypes usually associated with seawater and sediments not generally associated with hydrothermal fluid inputs. Mariana Cluster III is generally from much hotter vent sites and is dominated by sulfur-oxidizing ɛ-Proteobacteria. Quantitative-polymerase chain reaction (Q-PCR) of Archaeal abundance reveal that all of the microbial communities are dominated by members of the Bacterial domain. Sampling of microbial mats from Iceberg Vent at NW Rota-1 in 2004 and again in 2006 reveal the community has shown a transition from Caminibacter group ɛ-Proteobacteria phylotypes to a mixed population of Caminibacter, Sulfurovum, and Sulfurimonas group ɛ-Proteobacteria.