Several techniques have been used to identify and classify plants. We proposed Fourier transform infrared (FT-IR) spectroscopy, together with hierarchical cluster analysis, as a rapid and noninvasive technique to differentiate plants based on their leaf fragments. We applied this technique to three different genera, namely, Ranunculus (Ranunculaceae), Acantholmon (Plumbaginaceae), and Astragalus (Leguminoseae). All of these genera are angiosperms and include a large number of species in Turkey. Ranunculus and Acantholimon have ornamental importance, while Astragalus is an important pharmaceutical genus. The FT-IR spectra revealed dramatic differences, which indicated the variations in lipid metabolism, carbohydrate composition, and protein conformation of the genera. Moreover, cell wall polysaccharides including diverse groups could be identified for each genus. Acantholimon was found to have the highest hydrogen capacity in its polysaccharide and proteins. A higher lignin content. and a lower occurrence of decarboxylation and pectin esterification reactions were appointed for Ranunculus and Astragalus compared to Acantholimon. All these results suggested that FT-IR spectroscopy can be successfully applied to differentiate genera, as demonstrated here with Ranunculus, Astragalus, and Acantholimon. In addition, we used this technique to identify the same species from different geographical regions. In conclusion, the current FT-IR study presents a novel method for rapid and accurate molecular characterization and identification of plants based on the compositional and structural differences in their macromolecules.