The purpose of this article is to review the status of DNA assays used for the detection, identification, and individualization of Bacillus anthracis, Yersinia pestis, Francisella tularensis, Burkholderia mallei, and Brucella abortus. These select agent microorganisms are historically significant as they have either been used or experimented with as a bioweapon or as a terrorist agent and are the subject of intense research in the areas of biodefense and bioforensics. If the presence of a biological agent is suspected, sensitive and specific assays for rapid detection and identification are necessary. However, DNA methods for identification of the sample may also be applied in order to individualize the strain and potentially determine the source of the microorganism. Methods used at the Armed Forces Institute of Pathology (AFIP) for select agent microbial DNA analyses include DNA extraction, DNA quantitation, real-time polymerase chain reaction (real-time PCR) of genetic targets unique to the select agent microorganism, microbial 16S ribosomal RNA gene DNA sequencing, amplified fragment length polymorphism polymerase chain reaction (AFLP-PCR), and more recently, repetitive element polymerase chain reaction (REP-PCR) DNA fingerprinting. The methodologies of 16S ribosomal RNA gene DNA sequencing and DNA fingerprinting of microorganisms are well established within the field of diagnostic microbiology for DNA identification purposes, as well as DNA typing for epidemiological and genetic relatedness studies. 16S ribosomal RNA gene DNA sequencing and AFLP DNA fingerprinting have been validated at the Armed Force Institute of Pathology (AFIP) laboratory for identification purposes and can be used as a possible strain typing tool for Bacillus anthracis, Yersinia pestis, Francisella tularensis, as well as Brucella and Burkholderia species. The continued development and implementation of new DNA based methods with increased sensitivity and defined specificity will be particularly useful for the detection of residual microbial DNA signature in situations where the microorganism has been rendered nonviable by decontamination procedures or not able to be cultured on microbiological media.