Global microbiological diversity has increased dramatically due to advances in high-throughput sequencing technologies. Still, most recent studies have concentrated on samples with higher biomass; little is understood about the microbial diversity of habitats with lower biomass or atypical environments. Due to the possibility of discovering new physiologies, scientists are currently using genomic technologies to investigate low-biomass habitats. This has allowed us to gain a better understanding of the functioning mechanism of microorganisms living in extreme and unusual environments, as well as the consortia. Community genomics has provided data on the type and extent of recombination, differences in gene content, the level of genetic diversity in the oceans, interactions between viruses and hosts, the identification of new metabolic capabilities and taxonomic groups, and the distribution of organisms across environmental gradients. This chapter covers several molecular techniques for studying microorganisms at the genomic level.