Rapid identification of aerosolized biological agents following an alarm by particle triggering systems is needed to enable response actions that save lives and protect assets. Rapid identifiers must achieve species level specificity, as this is required to distinguish disease-causing organisms (e.g., Bacillus anthracis) from benign neighbors (e.g., Bacillus subtilis). We have developed a rapid (1-5 minute), novel identification methodology that sorts intact organisms from each other and particulates using capillary electrophoresis (CE), and detects using near-infrared (NIR) absorbance and scattering. We have successfully demonstrated CE resolution of Bacillus spores and vegetative bacteria at the species level. To achieve sufficient sensitivity for detection needs (~10 4 cfu/mL for bacteria), we have developed fibercoupled cavity-enhanced absorbance techniques. Using this method, we have demonstrated ~two orders of magnitude greater sensitivity than published results for absorbing dyes, and single particle (spore) detection through primarily scattering effects. Results of the integrated CE-NIR system for spore detection are presented.