We describe the ultra-fast and sensitive detection of the gene encoding the protective antigen of Bacillus anthracis the causative agent of anthrax. Our approach employs a highly novel platform technology, Microwave-Accelerated Metal-Enhanced Fluorescence (MAMEF), which combines the use of Metal-Enhanced Fluorescence to enhance assay sensitivity and focused microwave heating to spatially and kinetically accelerate DNA hybridization. Genomic and exosporium target DNA of Bacillus anthracis spores was detected within a minute in the nanograms per microliter concentration range using low-power focused microwave heating. The MAMEF technology was able to distinguish between B. anthracis and B. cereus, a non-virulent close relative. We believe that this study has set the stage and indeed provides an opportunity for the ultra-fast and specific detection of B. anthracis spores with minimal pre-processing steps using a relatively simple but cost-effective technology that could minimize casualties in the event of another anthrax attack.