A liquid chromatography–ion trap mass spectrometry method with three “time segments” has been developed to determine malachite green (MG) and its major metabolite, leucomalachite green (LMG) in edible goldfish muscle. By using the optimized “time segments”, MG and LMG as well as the internal standard atrazine-d 5 were analyzed with good sensitivity with positive ESI–MS in a single run. The homogenized fish muscle tissues were extracted with a solution of perchloric acid and acetonitrile, followed by partitioning with dichloromethane. Strata-x polymeric solid-phase extraction column was used for the clean-up process. The determination of MG and LMG was achieved by using a reversed-phase HPLC gradient program coupled with MS/MS in multiple-reaction-monitoring mode. Matrix calibration curves were linear over the ranges of 5–500ng/ml for MG and 1–100ng/ml for LMG. Recoveries of the fish tissue extraction at three spiked levels (2, 10 and 30ng/g for MG as well as 0.4, 2 and 6ng/g for LMG) were better than 71% and 89%, respectively. Relative standard derivations from six determinations were less than 8%. The method detection limits were 0.13ng/g for MG and 0.06ng/g for LMG.