The electrophoretic mobility of silica nanospheres was shown to be a function of separation conditions such as pH and phosphate concentration of a carrier electrolyte. The separation selectivity can be controlled by the separation conditions and optimised depending on the sample composition. The effects of pH and phosphate concentration of buffer solutions on the nanosphere electrophoretic mobility are explained using the Overbeek-Booth electrokinetic theory taking into account both electrophoretic retardation and the relaxation effect.