Bacillus anthracis and Yersinia pestis are at high risk of bioterrorism, but they have different strains of virulence that exist in the natural environment, making it difficult to diagnose the risk of disease. This study aimed to develop a novel hexaplex PCR assay to simultaneously detect B. anthracis and Y. pestis and quickly distinguish their virulence levels. The vrrA, pagA, and capA genes from B. anthracis and ypo2088, pla, and caf1 genes from Y. pestis were specifically amplified to generate six PCR fragments of 222, 751, and 610 and 103, 438, and 271 bp, respectively. Furthermore, a recombinant competitive internal amplification control was designed in the assay, which coamplified with the capA gene primer pairs, producing a fragment of 1000 bp in length. Thirtyeight bacterial strains including 4 reference strains and 34 screening strains derived from human, herbivores, and environments in the North of Vietnam, as well as spiked soil samples, were used to evaluate the assay. The new hexaplex PCR assay was in accordance with the conventional culture methods to detect B. anthracis and Y. pestis. In addition, this assay can be quickly discriminated among pathogenic and non-pathogenic B. anthracis and Y. pestis strains, as well as rapidly differentiate levels of virulence among strains isolated from human and soil samples in some areas of Vietnam. The new hexaplex PCR is a useful tool in screening for both pathogenic and non-pathogenic B. anthracis and Y. pestis, necessary in use for biodefense purposes and disease prevention.