Surface-enhanced Raman spectroscopy (SERS) can provide rapid fingerprinting of biomaterial in a nondestructive manner. The adsorption of colloidal silver to biological material suppresses native biofluorescence while providing electromagnetic surface enhancement of the normal Raman signal. This work validates the applicability of qualitative SER spectroscopy for analysis of bacterial species by utilizing principal component analysis (PCA) to show discrimination of biological threat simulants, based upon multivariate statistical confidence limits bounding known data clusters. Gram-positive Bacillus spores (Bacillus atrophaeus, Bacillus anthracis, and Bacillus thuringiensis) are investigated along with the Gram-negative bacterium Pantoea agglomerans.