The Luminex® xTAG technology is a medium to high throughput, open methodology able to test many single nucleotide polymorphisms (SNPs) in a single reaction and a minimum time. Multiplex SNPs interrogation are conducted on the Luminex xMAP system, which uses lasers to read universal tag, color-coded microspheres that attach to specific nucleic acid sequences. The present method describes a Multiplex Oligonucleotide Ligation-PCR procedure (MOL-PCR) for the simultaneous interrogation of 13 phylogenetically informative SNPs within the genome of Bacillus anthracis. The reported 13-plex assay enables efficient B. anthracis genotyping into major sublineages and groups. While cost-effective compared to other monoplex methods, the present MOL-PCR method also offers a high degree of flexibility and scalability. It can easily accommodate newly identified SNPs to increase resolving power to the canSNP typing of B. anthracis.