In this paper the conformational behavior and thermodynamics of radical scavenging action of alizarin (A) and alizarin red S (ARS) were investigated at the M06-2X/6-311++G(d,p) and M06-2X/cc-pVTZ levels of theory in the gas phase and water solution. For this purpose all BDE (bond dissociation enthalpy), IP (ionization potential), PDE (proton dissociation enthalpy), PA (proton affinity), and ETE (electron transfer enthalpy) values were calculated, implying that all radicals, anions, and radical cations issued from A and ARS were examined. Since it turned out that all thermodynamic parameters for A and ARS are mutually comparable, one can assume that the two compounds are of similar antioxidative capacity, implying that the influence of the sulfonate group is insignificant. It was shown that the hydroxyl group in position 2 of A and ARS is the preferential site for heterolytic and homolytic cleavage in both phases, as the negative charge and spin density in the formed anions and radicals are delocalized over the B ring. In spite of the fact that the IP values of A and ARS are significantly lower in water, SET-PT is not a favored mechanism of both molecules in either environment. On the other hand, HAT is the predominant reaction pathway of A and ARS in gas, whereas SPLET is the preferential mechanism in water.