Malachite green (MG) has been used world-widely in aquaculture as a parasiticide or fungicide. Although MG performed successfully, it has not been permitted for use in aquaculture from European Union, USA, and Canada because of its carcinogenicity and mutagenicity. We developed a sensitive and specific method to determine MG and its principal metabolite, leucomalachite green (LMG), respectively by isotope dilution liquid chromatography mass spectrometry (ID-LC/MS). To enhance the extraction recovery of MG and LMG from fish tissue, an additional step, saponification, was introduced in sample preparation process to remove fat in sample extract, which hampered the performance of SPE columns. The residue of MG and LMG in fish was analyzed using liquid chromatography mass spectrometry in the selected ion monitoring (SIM) mode by monitoring at m/z 329 and 334 for MG and $d_5$-MG and at m/z 331 and 337 for LMG and $^{13}C_6$-LMG, respectively. This method was validated by comparing with the value of the reference material provided by Laboratory Government Chemistry (LGC). The results agreed within the measurement uncertainty and the accuracy was much improved than the provided reference value by LGC.