A high performance capillary zone electrophoresis method was established for the determination of marbofloxacin drug substance. An untreated fused-silica capillary was used with 15mmol/L sodium borate buffer (pH 9.2) as running buffer at the detection wavelength of 295nm, separation voltage of 20kV and the injection volume of sample for 10s. The calibration curve for marbofloxacin is linear in the concentration range of 10~100μg/mL. The average recovery is 100.2% with RSD of 0.97%.