Malachite green (MG) has been widely used as the most efficacious antifungal agent in the fish farming industry. The aim of this study is to evaluate hepatotoxicity of different MG concentrations in edible fish, its mutagenicity and DNA damage on adult albino rats for 4 weeks. Forty eight adult male albino rats were utilized and equally divided into 4 groups, each contains 12 rats. Three concentrations 2.2, 30 and 60 μg/kg body weight (MG) were tested in three independent experiments for 4 weeks. Mutagenicity and hepatotoxicity were evaluated by biochemical, cytogenic, histopathological examination and DNA fragmentation. MG caused an increase of alanine aminotransferase, aspartate amino transferase (ALT and AST), alkaline phosphatase (ALP) levels, and decrease in total protein in animals treated with MG as compared to control. Also, all concentrations of MG were found to induce significant DNA damage in bone marrow cells as assessed by chromosomal aberration. The histopathological changes were highly significant in rats treated with higher doses than other groups and persist even after 2 weeks from MG stoppage. We can conclude that MG and its residues in the edible tissue of fish could not be ignored due to their suspected genotoxicity, hepatotoxicity and DNA fragmentation with apoptotic changes even at lower doses, posing a potential risk for human consumption. This leads us to put strict limitations on its use in the fish farming industry in Egypt.