Abstract Lipases (triacylglycerol acylhydrolases, E.C. 3.1.1.3) are enzymes widely applied in industry and medicine. Our previous study showed that Candida catenulata produced much higher lipase activity in presence of 150 mg fluconazole than that in untreated control. Consequently in this study, optimization of fluconazole-treated C. catenulata for maximum lipase production was carried out. Fluconazole-treated C. catenulate cultured on medium containing 2.5% Tween 80 as carbon source, 0.7% yeast extract as nitrogen source, and 10 mM CuSO₄.5H₂O. pH 5.5, dark incubation at 37 °C under dark agitation for 3 days expressed the optimum physiological variables for maximum lipase production. Transmission electron microscopy (TEM) of the native cell (control) of C. catenulata declared a typical morphology of Candida cell with a uniform central density, typical structured nucleus, and a cytoplasm with several elements of endomembrane system and enveloped by a regular intact cell wall. The TEM photomicrograph of 150 mg fluconazole-treated cells of C. catenulata showed that the ultrastructures of treated C. catenulata displayed many noticeable morphological changes. The effect of mutagens [sodium azide (SA), ethidium bromide (EtBr), ethanol (EtOH)] was assayed on the lipase activity from C. catenulata. All mutagenic compounds with different concentrations decreased the lipase activity. Yeast specific activity, protein concentrations, and dry biomass gradually reached their highest decline at mutagen-elevated concentrations. Combination of lower concentrations of mutagen (0.1 µg/ml EtBr + 0.5 mM SA + 10% EtOH, Comb-Fl) exerted synergistic inhibition action and reduced C. catenulata virulent factor (lipase) over their single treatment. When 150 mg fluconazole was added to the mutagen’s combination mixture (Comb + Fl), an increase in the production of the virulence factor lipase by C. catenulata was detected. This action indicated the antagonistic effect of fluconazole over the mutagen combination mixture in increasing the fungal pathogenicity.