In this paper, the dissociation constants (pKa(1), pKa(2)) of five anthraquinones were determined from the relation between the effective mobility at different pH values and the buffer pH value, which was derived from the basic electrophoresis theory and the dissociation equilibrium of a binary acid. in addition, the changes of pKa values of the five compounds were also investigated when organic modifiers were added to the buffer system.