Alexandrium tamarense is a notorious harmful algal bloom species, which is associated with the largest number of paralytic shellfish poisoning cases, causing devastating economic losses and health hazards. The marine bacterium Mangrovimonas yunxiaonensis strain LY01 showed high algicidal effects on A. tamarense. A. tamarense was also susceptible to the supernatant of LY01 as revealed by algicidal activity assay, but washed bacterial cells did not show algicidal activity towards A. tamarense. In this study, we investigated the algicidal effect of the supernatant on growth, photosynthesis and the antioxidative response of A. tamarense. The results indicated that under the algicidal effect of the supernatant, the contents of cellular pigments including chlorophyll a and carotenoids were significantly decreased, and the decline of the maximum quantum yield and relative electron transport rate values suggested that photosynthetic inhibition occurred in the photosystem II system. The content of reactive oxygen species (ROS) increased after 0.5 h exposure, and the surplus ROS induced lipid peroxidation, the destruction of cellular membrane integrity and decreased cellular protein and carbohydrate contents in the algal cells. At the same time, the supernatant also induced the responses of antioxidant enzymes and non-enzymatic antioxidant. The transcription of photosynthesis- and respiration-related genes were significantly inhibited during the exposure procedure, which obstructed photosynthetic efficiency and capacity and disturbed the respiratory system, thereby increasing ROS production again. All these results elaborate clearly the entire procedure by which cellular physiological levels respond to the algicidal bacterium and may contribute to a better understanding of the bacterial control of A. tamarense.