This research was carried out to separate of polyoxo-anions, P2Mo5, Mo7 and Mo8, by Capillary electrophoresis. The equilibrium conditions, stability and solubility of these polyoxoanions are also studied. The equilibrium depends both on the concentration and pH of the solution. Counter ions have also an effect on the equilibrium of these Polyoxomolybdate. The interaction of polyoxomolybdate with different counterions, namely Na+, K+, Li+ and NH4+, is also part of this study. This kind of interaction is important in determining POM properties and consequently their application. Their properties and structure can be also controlled by interacting with cations. The affinity of these cations with POM and their stability was observed from electropherogram. On other way, the interaction of POM with five specific amino acids is also characterized using CE. These five amino acids includes negatively charged (D-Aspartate and D-Glutamate), neutral (L-Leucine and L-Phenylalanine) and positively charged (L-Histidine) to study the effect of the charges of amino acids on interaction with diphosphopentamolybdate. Lastly, the interaction of Polyoxomolybdate with α-CD and β-CD is also studied. α), have optimal limits.