The characterization of Mexican cochineal in Mesoamerican codices is a challenge. Indeed, red anthraquinonic dyes are easy to detect, but it remains difficult to assess their precise origin (e.g. the insect specie) with strictly non-invasive techniques. Such class of dyes has been identified in most of the studied codices, and especially in the Codex Borbonicus where it has been used to generate a large number of hues along the codex. In order to understand how these different hues were obtained, it is important to understand the relationship between the colors of the anthraquinones and their chemical environnement. The work presented is part of a larger study that uses Vis-NIR reflectance spectroscopy to compare the coloring materials analyzed on the Codex Borbonicus with samples produced with traditional materials described in the Florentine Codex (the XVIth century bilingual spanish/nahuatl encyclopedia).