Molecular-phylogenetic methods have revolutionized the analysis of complex microbial communities. Polymerase chain reaction amplification and phylogenetic analysis of small-subunit ribosomal RNA gene sequences allow microbes to be identified objectively, even in the absence of cultivation. Furthermore, the sequence information obtained by these means can be used to design sequence-based tools for identifying, tracking, and diagnosing the presence of microbes in complex samples. In this article, we summarize this approach and review its application to the study of the human gastrointestinal microbiota. Although just beginning, molecular-phylogenetic surveys of human gut microbes have revealed that most microbes identified in the gastrointestinal tract represent novel, previously undescribed species. A full description of the microbial constituents of the human gut will set the groundwork for interpreting how the gastrointestinal microbiota influence the health of the host.