The present invention utilizes unique DNA signatures to identify Bacillus anthracis. The DNA signatures can also be used in other types of detection. These signatures have been found to be unique to Bacillus anthracis, and can be used to understand how these DNA regions are being used to make this species different from closely related Bacillus species. Mechanisms of virulence, invasion, evolution, interactions with other microbes, antibiotic resistance etc. can be investigated with these regions once they are known. The method comprises using a multiplex polymerase chain reaction analysis of separate loci on the Bacillus anthracis chromosome to produce a set of chromosomal DNA signatures, and using at least one of the chromosomal DNA signatures to detect genetically the Bacillus anthracis.
 The United States Government has rights in this invention pursuant to Contract No. W-7405-ENG-48 between the United States Department of Energy and the University of California for the operation of Lawrence Livermore National Laboratory.