Fiber optics reflectance spectroscopy (FORS) is commonly used to non-invasively identify madder- and cochineal-based pigments on works of art, but the significant shifts sometimes observed in the position of their diagnostic absorption features can hinder correct interpretation of the spectra. To better understand these shifts, and improve the ability to confidently identify these pigments, a systematic study was carried out to evaluate the effects of different pigment recipes and laking substrates on reflectance spectra. Sixteen different madder- and cochineal-based pigments were synthesized using historical recipes and painted in four different binding media (gum Arabic, linseed oil, beeswax, and egg yolk). The results of the study showed that, in contrast to the absorption features typically used for identification, features in the first derivative transformation of the FORS spectra provided a more robust means of primary identification. In addition, once it has been identified as cochineal, the absorption features in the spectra of cochineal-based pigments could be correlated to the recipe employed, providing a possible means for inferring the method of manufacture and laking substrate from a non-invasive analysis. The results of this study were used to create a decision tree for the identification of madder and cochineal pigments based solely on FORS. The presentation will walk the audience through the decision tree using several different case studies, while discussing the strengths and limitations of the method.