Conodonts and scolecodonts are common Paleozoic microfossils that are often used to determine the geothermometry of Paleozoic sequences. The two fossils, which can be difficult morphologically to distinguish one from the other, undergo a different thermal alteration pathway. In this study, Fourier transform infrared (FTIR) spectroscopy of scolecodont and conodont microfossils from the Woodford Shale of southern Oklahoma, United States, confirmed they have different chemical compositions. Infrared (IR) spectra acquired from conodonts show a predominance of an inorganic carbonated hydroxylapatite (CO3OHAp) with a minor organic composition of aliphatic hydrocarbon, containing carbonyl substituent functional groups. In contrast, IR spectra acquired from scolecodonts show no inorganic mineralogy but instead confirm that these microfossils are composed of organic material consisting of an aliphatic and aromatic hydrocarbon network with ether linkages and carbonyl substituent functional groups. These data reveal that scolecodont elements can easily be distinguished from conodont elements with FTIR microspectroscopy due to their different chemical compositions. This study provides future fossil workers with a viable method to independently identify enigmatic toothlike microfossils that cannot confidently be assigned to either scolecodont or conodont groups by morphology alone.