Much interest has been generated by the discoveries of biodiversity associated with seamounts. The volcanically active portion of these undersea mountains hosts a remarkably diverse range of unusual microbial habitats, ranging from black smokers rich in sulfur to cooler, diffuse, iron-rich hydrothermal vents. As such, seamounts potentially represent hotspots of microbial diversity, yet our understanding of the microbiology of seamounts is still in its infancy. Here, we discuss recent work on the detection of seamount microbial communities and the observation that specific community groups may be indicative of specific geochemical scenarios, such as iron and sulfur cycling. These observations are based on the metabolisms predicted by phylogenetic characteristics exhibited by the dominant populations found within these microbial communities as compared to the closest related isolate found in culture. Therefore, these studies combine the use of both cultivation-dependent and -independent analyses. Cultivation-independent studies were primarily completed using cloning and sequencing techniques targeting small subunit ribosomal gene (SSU rDNA) biomarkers along with similar biomolecular tools like terminal-restriction fragment polymorphism (T-RFLP) and quantitative polymerase chain reaction (Q-PCR), which allow for the determination of phylotypes (analogous to species). We discuss the notion of Zetaproteobacteria and/or Epsilonproteobacteria being the most common members of hydrothermal habitats associated with seamounts exhibiting volcanic activity. Another noneruptive seamount scenario is also examined, for example, South Chamorro Seamount, an active forearc serpentinite mud volcano.