Raman spectroscopy has been accepted as a useful tool for the characterization of natural products. However, to identify a specific compound in a mixture sample of natural products using Raman spectra alone is highly challenging if not impossible. We demonstrated an effective solution to such issues using a method combining statistical Raman spectroscopy and Mass spectrometry. The method was validated with a successful application to the identification of the major anthocyanin components in a purple yam (Dioscorea purpurea) extract. Of particular interest is that statistical grouping of the bioflavonoid standards that formed the database of this study was found to correspond closely to the conventional chemical classification. An initial theory on the chemical aspects of Raman spectroscopy pertaining to the connectivity of Raman-active functional groups in bioflavonoids was developed based on the statistical correlation between chemical classification and Raman spectroscopy.