The advent of molecular techniques has revolutionized our understanding of microbial ecology, and their use in environmental microbiology is widespread. Many of the recent studies investigating the microbial flora of diverse ecosystems have adopted a common approach of targeted amplification of gene sequences from total extracted DNA using the polymerase chain reaction (PCR) followed by cloning and sequence analysis of amplimers. The study of 16S rRNA gene sequences has dominated these studies (1,2). Such studies have developed so rapidly because of the availability of automated sequencing techniques, which greatly reduce the processing time of retrieved DNA molecules and allow the analysis of a sufficient number of clones to make findings more representative of the diversity present within a system. This chapter covers the principles and use of automated DNA sequencing systems.