Burkholderia andropogonis is the causal agent of bacterial leaf stripe in sorghum. Strict import quarantine regulations of numerous countries mandate a need for development of a rapid, reliable, and cost-effective diagnostic technique for the identification of B. andropogonis. Using a primer corresponding to the bacterial repetitive BOX element and PCR, we developed a DNA fingerprint which differentiated B. andropogonis from other phytobacterial pathogens.