Traditional methods for the analysis of soil processes are based on measuring and modeling the distribution of chemical compounds and determining their transformation rates. These approaches have formed the basis of our understanding of soil biogeochemical processes, and they have demonstrated the fundamental role of microbes in regulating these processes, but they do not provide a complete view of the complexity of the microbial contribution to soil function. Recent research has revealed the tremendous diversity of microorganisms responsible for catalyzing a variety of soil processes. Such functional redundancy within soil microbial communities may have significant impacts on process rates and ecosystem stability. Therefore, the analysis of functional diversity and its dynamics in the environment is essential for understanding the biogeochemistry of soil systems. Until recently, methodological limitations hindered investigation of the relationship between microbial diversity and soil processes. Over the last decade, innovative molecular approaches to the study of natural microbial communities and the functional genes responsible for biogeochemical processes have given us new insight into this relationship. One new approach, DNA microarray analysis, promises to be especially useful for the analysis of these functional genes.