Microbial communities are the basis for most, if not all, biochemical or biogeochemical functions in the environment.  These environments are vastly different with respect to matrix, function, and biodiversity, and as such, present minute to stark differences in their respective microbial communities.  The advent of polymerase chain reaction has brought with it an intimate knowledge of these communities and how they change spatially and temporally.  Application of 16S rRNA targeted and specific gene targeted PCR have culminated in identification of previously unknown and unculturable bacteria (>99% of all bacteria), and with current library preparations using metagenomic analysis, the amount of information available to microbial ecologists is vast and seemingly infinite.  The question is, “what do we do with all this data”.  Fortunately, newly available programs and cloud-based computing have allowed for analysis and drawing of meaningful conclusions from this information.  This review will serve to identify current accepted methodologies and future directions in culture-independent microbial community analysis.