Three kinds of traditional molecular methods are available for the detection of microbial community diversity: nucleic acid hybridization-based methods, PCR electrophoresis-based methods, and Sanger sequencing-based methods. Distinct from Sanger sequencing, high-throughput sequencing is based on the sequencing-by-synthesis principle and the massively parallel signature sequencing strategy, allowing the simultaneous determination of the sequences of millions of different DNA templates. Thus, the metagenome of an entire microbial community can be sequenced simultaneously, without the need to isolate unique sequences through clone library construction and subculturing. High-throughput sequencing-based methods are highly sensitive and specific, are inexpensive, and require relatively little time compared with traditional molecular methods for microbial diversity research. In the last section of this chapter, we introduce several traditionally used gene targets for microbial identification.