The Raman spectroscopy of Maya Blue (MB), a nanostructured organic-inorganic hybrid material, has received considerable attention. A re-evaluation of the Raman literature data for indigo dye, genuine MB samples and model specimens obtained by the binding of indigo to phyllosilicate clays, such as palygorskite and sepiolite, using chemometric analysis of normalised spectra is reported. Available data present features in support of the following ideas: (1) dehydroindigo accompanies indigo in MB; (2) different topological isomers, i.e. dye molecules attached to different coordinative sites of the palygorskite framework, are involved in MB; and (3) different procedures were probably used for preparing MB in ancient Mesoamerican civilisations.