This study was conducted to assess genotoxic and histopathological changes induced by some chemicals applied in aquaculture as Oxytetracycline (OTC) from the antibiotics group, Malathion (MAL) from the pesticides group, or Formalin and malachite green [D1] [MF2] [MF3] FMG from disinfectants group in Nile tilapia (Oreochromis niloticus) culture as a model of toxicological studies in aquatic surroundings. Fish were exposed to OTC in a dose of 80 mg ̸ kg/biomass/day, MAL in a dose of 0.1 ppm, or FMG in a dose of 100 ppm and 0.2 ppm respectively for 21 days. The genotoxic effect was determined through DNA damage detection by comet assay as revealed a significant increase in tail length, tail DNA%, and tail moment, all chemicals revealed DNA damage when compared to control. qPCR revealed significant (p <0.05) down regulation of immunity-related genes, MHC IIA, Tlr7, and IgM heavy chain in head-kidney and significant (p <0.05) upregulation in the expression level of the inflammatory gene,  TNF-α, in liver tissue of all chemicals treated groups in comparison with a control group. Histopathological examination of liver and kidney revealed hepatocyte and renal damage.  [D1]Is malachite green  [D1]is still applied in aquaculture in Egypt? It is  banned in many countries worldwide  [MF2]Used in fish hatcheries under restricted rules, and use only Zinc free malachite green  [MF3]