The primary objective was to identify and clone novel chromosomal DNA fragments for use as B. anthracis-specific markers. Towards this goal, 300 random primers (RAPD technology, randomly amplified polymorphic DNA) were screened to identify polymorphic loci on the anthrax chromosome. Five such DNA fragments uniquely amplifying from anthrax chromosome were identified and isolated. These fragments were cloned in pCR vector and sequenced. Database (genebank) analysis of one of the cloned probe, VRTC899, revealed the presence of specific chromosomal DNA probe, Ba813 from anthrax. This prove also contains flanking DNA with no homology to known sequences. Availability of signature DNA probes for detection of antrax-causing agent in environmental samples is critical for field application of DNA-based sensor technologies. In conclusion, we have demonstrated application of RAPD technology for identification of anthrax-specific signature sequences. This strategy can be extended to identify signature sequences from other BW agents.