Abstract: This invention relates to methods for rapidly evaluating and identifying a microorganism of interest. A preferred method comprises (1) providing a plurality of said microorganism to a flow cytometer, wherein the plurality of said microorganism are labeled with a fluorescent marker; (2) obtaining from the flow cytometer fluorescence and scatter signals to generate a profile of said microorganism; and (3) comparing the profile thus generated to a signature profile of a reference microorganism. This invention is also directed to a microorganism evaluation system which comprises (1) a means for gathering fluorescence and scattering signals of a microorganism of interest; and (2) a means for comparing said fluorescence and scatter signals to a signature profile of a reference microorganism.