Biomarkers and other ancient preserved molecules are rapidly being discovered and used to study the evolution of life on Earth. We report the existence of echinoderm-specific organic molecules from different lower Mississippian (340 Ma) crinoid species that occur in the same sedimentary bed. These are the oldest examples of biomarker molecules extracted directly from fossilized remains. These biomarker molecules appear to resemble aromatic or polyaromatic quinones, based upon ultraviolet and visible light spectroscopy, fluorescence excitation-emission matrix spectroscopy, and electrospray ionization time-of-flight mass spectrometry. Results suggest that the preservation of diagnostic organic molecules is much more common that previously realized, and that preserved organic molecules may provide an independent method to unravel phylogenetic relationships among echinoderms and, perhaps, other fossilized organisms.