A method has been developed for the simultaneous determination of malachite green, gentian violet and their leuco-metabolites in various aquatic products using isotope dilution liquid chromatography–linear ion trap mass spectrometry without post-column oxidation. Sample was extracted with McIlvaine buffer and acetonitrile, followed by partitioning with dichloromethane, purified on basic alumina and OASIS MCX SPE column, and finally analyzed by LC–ESI–MS/MS with the select reaction monitoring (SRM) mode. Decision limits (CC α, α = 0.01) and detection capability (CC β, β = 0.05) of the method were in the range of 0.02–0.09 and 0.04–0.13 μg/kg for MG, GV, LMG and LGV in grass carp, eel, salmon, shrimp and shellfish, respectively, recoveries of MG, GV, LMG and LGV at all fortification levels (0.25–10 μg/kg) were from 80.8% to 115.7%, inter-day relative standard derivations were from 1.9% to 18.4%. This method appeared suitable for the control of MG, GV, LMG and LGV residues in aquatic products.