Sulfonated anthraquinones are precursors of many synthetic dyes and pigments, recalcitrant to biodegradation and thus not eliminated by classical wastewater treatments. In the development of a phytoremediation process to remove sulfonated aromatic compounds from industrial effluents, the most promising results have been obtained with Rheum rabarbarum (rhubarb), a plant species producing natural anthraquinones. Rhubarb is not only able to accumulate, but also to transform, these xenobiotic chemicals. Even if the biochemical mechanisms involved in the detoxification of sulfonated anthraquinones are not yet fully understood, they probably have cross talks with secondary metabolism, redox processes, and plant energy metabolism. Therefore, key problems of xenobiotic detoxification are addressed, as well as the potential role of the apoplast, often neglected, and the possible links with plant sulfur metabolism.