Limonoids found to be chemotaxonomic markers from the plants of the Meliaceae and Rutaceae families. In the present study, rapid identification of limonoids from Cipadessa baccifera and Xylocarpus granatum were achieved using fast and simple electrospray ionization quadruple time-of-flight mass spectrometry (ESI-Q-ToF-MS/MS) in positive-ion mode. Although the structures of these compounds were found to be similar, Collision Induced Dissociation (CID) mass spectrometric analysis of these protonated/sodiated molecules indicated different fragmentation patterns by which the structures were confirmed. The fragment ions were formed due to the loss of neutral components like H2O, CO2, methanol, as well as McLafferty rearrangement and Retro-ene reaction. Furthermore, MS/MS spectra revealed different fragmentation pathways for different classes of limonoids which further aided dereplication.