Abstract: A method for the evaluation of the uncertainty of malachite green,crystal violet,leuco malachite green and leuco crystal violet residues in aquatic products by ultra performance liquid chromatography-stable isotope dilution mass spectrometry was established. According to the determination of malachite green and crystal violet residues in aquatic product(GB/T 19857-2005),the mathematical models of uncertainty was established and the sources of uncertainty were analyzed. As a result,the main sources of uncertainty in measurement results were the preparation of standard solution and the standard curve fitting,isotope dilution method can reduce the sources of uncertainty introduced by the pretreatment process and matrix effect. The residue of MG in aquatic products was 14.26 μg/kg,the expanded uncertainty was 1.35 μg/kg(k=2). The residue of CV was 15.28 μg/kg,the expanded uncertainty was 1.29 μg/kg(k=2).The residue of LMG was 14.47 μg/kg,the expanded uncertainty was 1.21 μg/kg(k=2).The residue of LCV was 14.69 μg/kg,the expanded uncertainty was 1.24 μg/kg(k=2).