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Background: Fruits of Hunteria umbellata(HU) have been utilized in folk medicine as potent against Staphylococcus aureus(SA) infections, particularly skin and nasal related conditions. However, there is scarcity of literature concerning toxicological evaluation of graded doses of HU fruit, especially at molecular level, specifically targeting the accessory gene regulator (AGR) system to prevent abuse of doses in the treatment of bacterial infections. This research evaluated molecular toxicological property of SA exposed to varied concentrations of aqueous HU fruit extract ranging from 500 to 3.90625 µg/µL using broth microdilution method and quantification of AGR I and II genes’ expression employing two-step reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). We first identified quality and quantity of chemical compounds in aqueous fruit of HU using phytochemistry and hybrid gas chromatograph–mass spectrometer (GC–MS) technique. Additionally, preliminary bactericidal potential of HU was assessed before molecular toxicology. Results: Results revealed six phytochemicals and twenty analytical grade compounds from a standard library were identified from chromatograms of HU fruit extract. Some main compounds detected are n-Hexadecanoic acid (25.24%), 2-Pentadecanone, 6,10,14-trimethyl (16.08%), Cuparene (16.63%), Tetradecanoic acid (6.21%) and 9-Octadecenoic acid, (E)- (5.70%). Bactericidal activity shows significant (p< 0.05) toxicity in the tested (8) concentrations of HU fruits in a dose-response relationship compared to the controls (positive and negative). The quantified expression of AGR I and II genes in SA was most significantly increased (p< 0.05) at both 250 and 500 µg/µL of HU fruit extract while least significant increase (p< 0.05) was recorded at 125 µg/µL compared to control. Conclusions: Notably, the study highlighted a potential risk of augmented bacterial infection especially with higher doses of HU extracts during boils’ treatment and other epidermal infections instigated by Staph. Expression of both AGR genes at higher doses (250 and 500 µg/µL) is indicative of further expression of several other genes responsible for virulence factors in a variety of human bacterial infections. Thus, consumption of HU fruit to treat boils and blisters should be with great caution especially at high doses.