The awareness of the threat of Bacillus anthracis, the causative agent of the disease anthrax, as a biowarfare and bioterrorism weapon has revived the development of new technologies for rapid and accurate detection of virulent isolates in environmental and clinical samples. Here we explore the utility of molecular beacon real-time PCR technology for detection of virulent Bacillus anthracis strains. Molecular beacons are nucleic acid probes with high specificity, that act as switches by emitting fluorescence when bound to their nucleotide sequence targets by means of altering their conformation. In this study, five molecular beacons targeting Bacillus anthracis capA, capB, capC, lef, and pag alleles were designed and used in five uniplex assays. Another molecular beacon targeting the Bacillus group chromosomal 16s rRNA allele was designed for use in a duplex assay with an internal PCR amplification control. The molecular beacons were used in a real-time PCR assay for the detection of and differentiation between virulent B. anthracis and other members of the B. cereus group at the molecular level. Various B. anthracis samples as well as other bacterial and human samples were used to demonstrate the sensitivity and specificity of this assay. Use of the molecular beacon real-time PCR technology should accelerate current efforts to swiftly detect B. anthracis strains and its virulence plasmids in clinical and environmental samples and may extend to the development of additional molecular beacon-based assays for the identification of other pathogenic agents or the identification of B. anthracis directly from clinical samples.