Molecular biological techniques have revolutionized the field of geomicrobiology by providing researchers with robust techniques for identifying microorganisms and characterizing microbial communities in a wide variety of environments. These techniques have freed researchers from the constraints of classical culture-based microbiology and allowed the discovery of previously unknown phylogenetic diversity of microorganisms. In this chapter, we discuss the theory, methods, and workflow for applying molecular techniques to identify and characterize microbial populations. Our chapter focuses on SSU rRNA gene-based approaches, guiding the reader from sample collection and gene amplification through bioinformatics and statistical analysis. The workflow presented has been successfully used to identify microbial populations and community dynamics in a wide variety of habitats to understand the interactions between microbes and their environment.