In the past few decades, researchers have been examining natural microbial communities with a variety of culture-independent methods. These methods have also been applied to the study of microbial communities impacted by anthropogenic activity. Microbial communities are of interest because of their innate metabolic activities that can be exploited for a variety of beneficial purposes, such as the remediation of harmful pollutants. This manuscript reviews three widely used culture-independent methods as applied to the field of bioremediation (sequencing of rDNA clone libraries, terminal restriction fragment length polymorphism, and microarrays). These techniques are economically feasible and appropriate for undergraduate researchers. Each technique is briefly explained before case studies of their successful applications in bioremediation are reviewed. Drawbacks of each method are also presented. The advancement of microbial community analysis techniques in the future is discussed.