To monitor and assess the residues of malachite green (MG) and its metabolites leucomalachite green (LMG) and nitrofuran metabolites in mandarinfish and snake head mullet of Guangdong Province.Methods The residues of MG and its metabolites LMG and nitrofuran metabolites in muscle were measured by high performance liquid chromatography tandem mass spectrometry (HPLC-MS). Results The total detection rate of MG was 11.7% in 2013, and the total detection rate of nitrofuran metabolites was 20% in 2013. The total detection rate of MG was 25% in 2014, and the total detection rate of nitrofuran metabolites was 12.5% in 2014. The MG residues ranged from 0.58 to 19.1 μg/kg in the past two years, and the nitrofuran metabolites residues ranged from 0.66 to 36.6 μg/kg. The exposure assessment showed that the average daily exposure of nitrofuran metabolite in body might be 0.34 μg, that is 0.005 μg/kg BW, the maximum exposure might be 0.87 μg, that is 0.01 μg/kg BW, the average daily exposure of furazolidone metabolite in body might be 0.56 μg, that is 0.009 μg/kg BW,the maximum exposure might be 2.10 μg, that is 0.03 μg/kg BW, the average daily exposure of malachite green might be 0.24 μg or 0.004 μg/kg BW, and the maximum exposure might be 1.10 μg or 0.02 μg/kg BW.Conclusion The detection rate of MG and nitrofuran metabolites in mandarinfish and snake head mullet was relatively low. Dietary assessment showed that the risk of malachite green exposure was minimal.