Sulfonated anthraquinones are precursors of a large family of synthetic dyes and pigments, recalcitrant to biodegradation and thus not eliminated by classical wastewater treatments. In the development of a phytotreatment to remove sulfonated aromatic compounds from dye and textile industrial effluents, it has been shown that rhubarb (Rheum rabarbarum) and common sorrel (Rumex acetosa) are the most efficient plants. Both species, producing natural anthraquinones, not only accumulate, but also transform these xenobiotic chemicals. Even if the precise biochemical mechanisms involved in the detoxification of sulfonated anthraquinones are not yet understood, they probably have cross talks with secondary metabolism, redox processes and plant energy metabolism. The aim of the present work was to investigate the possible role of cytochrome P450s and peroxidases in the detoxification of sulfonated anthraquinones. Several plant species were thus cultivated in a greenhouse under hydroponic conditions, with or without sulfonated anthraquinones. Plants were harvested at different times and either microsomal or cytosolic fractions were prepared. The monooxygenase activity of cytochrome P450 toward several sulfonated anthraquinones was tested using a new method based on the fluorimetric detection of oxygen consumed during cytochromes P450 catalyzed reactions. Peroxidase was measured by spectrophotometry, with guaiacol. Results indicate that the activity of cytochromes P450 and peroxidases increased in rhubarb leaves, but not in leaves from common sorrel, when plants were cultivated in the presence of sulfonated anthraquinones. On the other hand, cytochromes P450 were able to accept as substrates anthraquinones containing sulfonated group in different positions, indicating that this enzyme was probably the first step in the metabolism of these xenobiotic compounds. These results support the idea that natural biodiversity should be better studied to use the most appropriate plant species for the phytotreatment of a specific organic pollutant.