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An automated method had been developed for the determination of Malachite green and Gentian violet as well as their leuco-metabolites in shrimp and salmon by liquid chromatography-tandem mass spectrometry with accelerated solvent extraction and auto solid-phase clean-up. The target analytes were extracted using accelerated solvent extraction (ASE) and then purified using auto solid-phase clean-up. The ASE conditions as: solvent, temperature, pressure, static time, and cell size were optimized. The optimum extraction conditions were set as the following aspects: using 22 mL ASE cell, McIlvaine buffer (pH 3)/acetonitrile/hexane (2/10/2, v/v) as the extraction solvent; pressure at 1500 psi; temperature at 60 °C; static time 5 min (static time); one cycles. The extracts were purified on OASIS MCX SPE column. Detection and quantification of Malachite green; gentian violet; leucomalachite green; leucogentian violet were performed by reversed-phase liquid chromatography coupled with electrospray ionization triple quadrupole mass spectrometry (LC-ESI-MS/MS). An averaged decision limits (CCα) and detection capability (CCβ) of the method were in the range of 0.005 μg/kg ～ 0.012 μg/kg and 0.08 μg/kg～0.13 μg/kg in shrimp and salmon. The recoveries of Malachite green; Gentian violet; Leucomalachite green; Leucogentian violet at levels of 0.1–1.0 μg/kg averaged from 82.1 to 102.9% with the relative standard derivation less than 14.6%. This method is precise, sensitive and highly efficient in extraction. What’s more, after routine applications, it’s turned out that this method is suitable for the determination of Malachite green, Gentian violet and their leuco-metabolites in shrimp and salmon.