Uniconazole, as a plant growth retardant, can enhance stress tolerance in plants, possibly because of improved antioxidation defense mechanisms with higher activities of superoxide dismutase (SOD) and peroxidase (POD) enzymes that retard lipid peroxidation and membrane deterioration. These years much attention has been focused on the responses of antioxidant system in plants to uniconazole stress, but such studies on aquatic organism are very few. Moreover, no information is available on growth and antioxidant response in marine microalgae to uniconazole. In this paper, the growth and antioxidant responses of two marine microalgal species, Platymonas helgolandica and Pavlova viridis, at six uniconazole concentrations (0–15 mg L−1) were investigated. The results demonstrated that 3 mg L−1 uniconazole could increase significantly chlorophyll a and carbohydrate contents of P. helgolandica (P < 0.05). Higher concentrations (≥12 mg L−1) of uniconazole could inhibit significantly the growth, dry weight, chlorophyll-a and carbohydrate contents of P. helgolandica and P. viridis (P < 0.05). Uniconazole caused a significant increase in lipid peroxidation production (MDA) at higher concentrations (≥ 9 mg L−1). The activities of antioxidant enzymes, superoxide dismutase (SOD) and catalase (CAT) were enhanced remarkably at low concentrations of uniconazole. However, significant reduction of SOD and CAT activities was observed at higher concentrations of uniconazole.