Soils are one of the most biologically diverse ecosystems on this planet. Since this diversity is mainly microbiological, analytical methods were often limited until molecular biological approaches were discovered. Many different approaches are now being used to gain a better understanding of soil microbial communities. One of these methods, denaturing gradient gel electrophoresis (DGGE) of target genes amplified by PCR will be described and examples of its use in soil community analysis will be given. PCR based methods eliminates the need to cultivate microorganisms; instead DNA can be extracted directly from environmental samples to examine the soil community in its entirety. The rRNA genes have been the most commonly used PCR targets for phylogenetic analysis of communities. The gradient of denaturants in the electrophoresis gel separates the PCR products by their sequence composition producing a genetic fingerprint. Spatial and temporal comparisons of soil communities from a variety of environments have been made using these fingerprints. Similarity between two communities has been quantified by evaluating the presence and absence of bands in the fingerprints. Multivariate analysis has been used to identify potentially significant populations within communities. There are also method limitations that must be considered before use this approach. For example, population richness of soil microbial communities often exceeds the resolving power of the method making it difficult to go beyond qualitative analysis. It may be possible to overcome this problem by using primer pairs that will amplify only a subset of the community. Nevertheless, the rapid high throughput nature of this method allows comparisons of numerous samples providing soil scientists a means to begin addressing complex ecological questions.