The microalga Botryococcus braunii has been studied for its hydrocarbon biofuel production potential. The range of the lipids it synthesizes cannot be readily profiled, because their main chemical class standards (long chain al-kenes and botryococcenes) are at present unavailable. The aim of this study was to develop a direct, specific GCMS analysis method for the rapid chemotyping of these lipids. The SIM (Selected Ion Monitoring)-GCMS program we developed discriminates classes and subclasses of the targeted molecules through their main chemical motifs identified with fragment ions of specific m/z selected by unsupervised chemometrics. Our validation results indicate that the SIM mode enhanced their detection by significantly increasing the signal-to-noise ratio ca. 20-fold. The profiling results from TL extracts of diverse B. braunii strains show that under the culture conditions tested, these strains could be distinguished by their chemical signatures, which also signaled different culture conditions involving various physiological states. We were able to make a rapid estimate of the biofuel potential of these strains, focusing on alkenes and botryococcenes. The direct injection SIM-GCMS method was successfully applied here for rapid chemotaxonomy, displaying good sensitivity and specificity for new high molecular weight hydrocarbons from B. braunii.