A liquid chromatography/tandem mass spectrometry (LC/MS/MS) method was developed for determining the residues of malachite green (MG) and leucomalachite green (LMG) in a number of aquatic species. MG and its metabolite were extracted from homogenized tissues with a perchloric acid-acetonitrile solution; the extract was centrifuged; and an aliquot was taken, concentrated, and passed through a chemically bonded octadecyl C18 solid-phase extraction column. The compounds of interest were eluted with acetonitrile, and the eluate was evaporated to dryness. The residue was dissolved in acetonitrile and diluted with water in preparation for analysis by LC/MS/MS. MG and its metabolite were determined by reversed-phase LC using a Luna C18 column with an ammonium hydroxide-formic acid buffer in acetonitrile gradient and MS/MS detection using multiple reaction monitoring. Calibration curves were linear for all analyses between 5 and 500 pg injected for both analytes, with recoveries ranging from 81% for LMG to 98% for MG in salmon spiked at the 1 ng/g level. Detection limits of 0.1 ng/g for both MG and LMG were easily obtainable using the recommended method. The operational errors, interferences, and recoveries for spiked samples compared favorably with those obtained by established methodology. The recommended method is simple, rapid, and specific for monitoring residues of MG and LMG in a number of aquatic species.