A series of reversed phases bonded with several functional groups was investigated for separation of anthraquinone derivatives, following the previous work, dedicated to the selectivity of octadecyl silica bonded phases. Considering wide diversity of substitutions in hydrophobic anthraquinone skeleton, interactions like dipole–dipole, π–π or H-bond acceptor/donor, as well as inclusion complexes formation can be employed to improve separation. In this study, several phases with grafts like cyano, nitro, aromatic, PEG, diol, calixarene and cyclodextrin were used with water–acetonitrile gradient for separation of thirty anthraquinoids’ standards. The evaluation of performances was measured using the symmetry parameter and the number of critical pairs of peaks formed. The results point out the aromatic and calixarene bonded silica as the most interesting in terms of symmetry and critical pairs number. Finally we tested the performance of Caltrex Resorcinaren, Pursuit XRs DP and Luna Phenyl-Hexyl on real samples of anthraquinone natural dye extracted from a red thread taken from a 15th C. tapestry. We observed and compared the retention behaviour of some new anthraquinoids additional to our standards set and showing behaviour particular to substituted anthraquinone carboxylic acids.