Capillary zone electrophoresis is proposed for the determination of magnesium and calcium ions in seawater. A carrier solution containing EDTA was adopted for the complexation of these ions and the effect of sodium chloride concentration in the sample solutions on the results was examined. It was found that magnesium and calcium ions could be determined without any pretreatment by injecting 100-fold diluted seawater samples. Linear calibration graphs were obtained for standard solutions containing up to 10.0 mg/l of calcium ion when both peak area and peak height were used. On the other hand, a linear calibration graph was obtained for standard solutions containing up to 20.0 mg/l of magnesium ion when the peak area was used, while a curved one was obtained when the peak height was used. Relative standard deviations were 0.8 and 1.2% when a standard solution containing 5.0 mg/l of magnesium and 8.0 mg/l of calcium ions was analysed 8 times using the peak area. Limits of detection for magnesium and calcium ions were 0.13 and 0.26 mg/l, respectively. The proposed method was applied to the determination of magnesium and calcium ions in surface and bottom seawater samples.