Background: Hesperidin and myricetin are anti-inflammatory and anti-oxidant flavonoids that have beneficial effects in fatty liver disease (FLD), but information regarding their effects on cytochrome P450 (CYP450) enzymes in FLD is limited. Objectives: This study determined the impacts of hesperidin and myricetin on CYP450 profiles in FLD mice. Materials and Methods: Adult female mice were fed a high fat diet (HFD, 60 kcal % fat of total food) with daily intragastrically administered ethanol (0.5 g/kg/day) in combination with either fenofibrate (40 mg/kg/day), hesperidin (50 and 200 mg/kg/day), or myricetin (50 and 200 mg/kg/day) for 60 consecutive days. Liver histomorphology was examined by oil red O staining. Hepatic enzyme activity and mRNA expression of CYP1A2, CYP2E1, CYP3A11, CYP3A13, and CYP4A11 were assessed. Results: HFD-induced hepatocellular damage was prevented by low dose hesperidin and myricetin. Expression of Cyp1a2, Cyp2e1, and Cyp4a11 mRNAs as well as CYP2E1 and CYP3A activities was significantly induced by HFD plus ethanol (HE) while Cyp3a13 expression was slightly increased. Fenofibrate and low dose hesperidin prevented HE-induced Cyp1a2 and Cyp2e1 expression while HE-induced Cyp4a11 expression was prevented by all treatments. The expression of Cyp3a13 was extensively suppressed by high-dose hesperidin and myricetin, and CYP2E1 and CYP3A activities were significantly decreased by all treatments. Conclusion: Alteration of CYP450 profiles by high doses of hesperidin and myricetin could lead to drug interactions. Nevertheless, low dose hesperidin prevented dysregulation of CYP450 expression in FLD and is a promising candidate for FLD treatment.