Enrofloxacin (ENR) and its metabolite ciprofloxacin (CIP) were determined by capillary zone electrophoresis (CZE) with end-column amperometric detection. The effect of several factors, such as pH and concentration of running buffer solution, separation voltage, injection time, and working potential, on CZE were investigated to establish the optimal conditions of separation and detection. Under a given set of conditions (pH 8.00 phosphate buffer solution (20 mmol/L); +0.95 V for the working potential; 18 kV for the separation voltage; sample injection at 18 kV for 10 s), the compounds investigated can be well separated and detected within 8 min. Excellent linearity was observed between peak currents and concentration of analytes in the range from 0.034 to 70.0 mg/kg for these two compounds. The detection limits (S/N= 3) for enrofloxacin and ciprofloxacin were 13.68 mg/kg and 14.35 mg/kg, respectively, which were about 7-fold lower than the maximum residue limits (MRLs) established by the European Union. A simple sample pretreatment method was developed and proved to be effective in obtaining good recoveries and short analysis time. The developed CE-AD method was simpler, faster, and less cost intensive than other reported methods, and allows the determination of ENR and its metabolite CIP in contaminated eel liver samples and other animal tissue samples at the required maximum residue limits.