The use of malachite green (MG) in fish farming is prohibited in China due to its potentially toxicological and carcinogenic nature, but it is still illegally used in some places. The aim of this study was to investigate the time and concentration-dependent responses of xenobiotic metabolizing and detoxification-related genes in diverse fishes exposed to MG both in vivo and in vitro. Experimental fish were administered to two exposure groups of malachite green (MG) (0.10 and 0.50 mg L⁻¹) for 8 h. The hepatocytes isolated from Nile tilapia were incubated with MG (0.5, 1.0, and 2.0 mg L⁻¹) for 8 and 24 h, respectively. In vivo, exposure to 0.10 and 0.50 mg L⁻¹ MG for 8 h caused significant changes of the detoxification-related genes on the mRNA expression levels. Low-concentration (0.10 mg L⁻¹) level of MG induced significant increase on the mRNA expression level of GSTR gene in Nile tilapia and other fishes. The mRNA expression of grass carp UCP2 was significantly induced when exposed to 0.5 mg L⁻¹ MG. However, the mRNA expression levels of GSTA, CYP1A, and GPX were inhibited significantly by 0.5 mg L⁻¹ MG in Nile tilapia, grass carp, and Taiwan snakehead. In vitro, the significant increase of mRNA expression of these genes was detected after exposure to 0.5 mg L⁻¹ MG (UCP2), and 1.0 mg L⁻¹ MG (CYP1A1, GSTA, GSTR, and UCP2). The induction of hepatic CYP1A1, GSTA, GSTR, and UCP2 in response to MG suggested a potential role of fish CYP1A1, GSTA, GSTR, and UCP2 in MG metabolism.