Rapid identification of Bacillus spores has attracted great interest in the medical and forensic communities due to the highly pathogenic nature of certain Bacillus species and its potential application in bioweapons. In this study, we evaluated the feasibility of rapid and reliable identification of several Bacillus spp. (B. subtilis, B. cereus, B. megaterium, B. pumilus, and B. sphaericus) using online MALDI-TOF mass spectrometry combined with lipid profiling. The bacterial cultures in liquid medium were extracted with methanol and chloroform, and the extracts were aerosolized into droplets and immediately analyzed with an online MALDI-TOF mass spectrometer. Results showed that phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and diglycosyldiacylglycerol (DGDG) were present in the mass spectra, as alkali metal adducts. The unique lipid profiles obtained from these Bacillus spp. allowed us to differentiate between them. The reliability and reproducibility of the rapid identification method for Bacillus were tested under different experimental conditions. An alternative online chemotaxonomic method for bacterial identification is demonstrated.