This is a new era for research in terrestrial ecology. As with diagnostics and research in medicine and forensics, molecular biology, the way the authors pose hypotheses, conceptualize experiments, and conduct research in rhizosphere ecology has been transformed. Many soil-borne organisms are morphologically indistinguishable, can change morphology from one sexual state to another, or are not culturable in vitro. These properties hinder the understanding of rhizosphere structure and function. Contemporary, molecular-based methods to isolate DNA from soil organisms will enhance the ability to track, identify and quantify individuals. The purpose of the chapter is to present a primer of basic methods that have direct application to recovery of DNA from mycorrhizal fungi in soils.