Malachite green is widely used in aquaculture as a biocide and also in food, health, textile and other industries. It controls fungal and protozoal infections and some other diseases caused by helminths on fish and other aquatic organisms. However, malachite green become one of the most controversial compound due to its toxic effects. It causes carcinogenesis, mutagenesis, chromosomal break, teratogenicity and respiratory toxicity. Histopathological effects of malachite green include multi-organ tissue damage and alterations in biochemical and haematological parameters of the blood. Toxicity of malachite green also occurs in some mammals, including organ damage, mutagenic, carcinogenic and developmental abnormalities. Residues of malachite green and its reduced form, leucomalachite green have been reported from liver, kidney, muscles as also from eggs and fry of fish. However, despite wealth of information on its toxic effects, it is still being used as a parasiticide in aquaculture and other industries. To counter act its toxicological effects, it is important to identify its alternative parasiticides, like humic acid, chlorine dioxide and Pyceze to replace malachite green.