A liquid chromatography/tandem mass spectrometry (LC-MS/MS) method was developed to quantitate and confirm the presence of malachite green and leucomalachite green in water using isotope internal standard dilution technique. Water samples were spiked with deuterium labeled isotope internal standards, extracted and cleaned by SPE of SCX column. Quantitative results were based on MRM. The calibration curve of malachite green and leucomalachite green showed good linearity in the range of 0.2 - 5 microg/L with correlation coefficient of 0.9993 and 0.9991 respectively. The detection limits of the method were 0.001ng/L for both malachite green and leucomalachite green. The average recoveries at three dose levels (0.2, 5 and 10 ng/kg) ranged from 93.6% - 107.5% with RSD from 3.7% to 9.3%. The method could identify and quantify malachite green and its metabolite leucomalachite green in fish pond water with satisfactory sensitivity, accurate and precision.