The diversity of organisms inhabiting soils has made it a challenging ecosystem to characterize and understand. On the other hand this diversity represents one of the greatest untapped resources on this planet. The role of soil biota in nutrient cycling has been long recognized in agricultural and environmental sciences but now their biotechnological, medical, and industrial uses are being discovered. Much of this has been aided by the application of molecular biological approaches to investigate soil ecosystems. These approaches eliminate the need to cultivate organisms, which has stymied studies in the past. One aspect of these investigations has been to understand the ecology of soil communities, which can be composed of organisms belonging to all three domains, the Bacteria, Archaea, and Eukarya. Investigators are now able to address a variety of questions about communities such as: the identity of dominant biota, phylogenetic diversity and abundance of specific biota, spatial distributions, temporal changes, and differential impact of perturbations. The method and more commonly multiple methods employed are dictated by the desired depth of understanding of these questions. Some of the more commonly used nucleic acids based methods for community analysis are: DNA:DNA reassociation kinetics, nucleic acid hybridization (including FISH and microarrays), metagenome sequence analysis, denaturing gradient gel electrophoresis (DGGE), terminal fragment length polymorphism (T-RFLP), ribosomal intergenic spacer analysis (RISA), and sequence analysis of 16 rRNA gene clone libraries. Many of these molecular based methods are rapid high throughput technologies that require little starting material, which has permitted scientists to address fundamental ecological questions. Additionally, the abundance of data that can be obtained has enabled comparisons of numerous samples providing soil scientists a means to begin addressing complex ecological interactions.