Heavy metal pollution in aquatic system is becoming a serious problem worldwide. In this study, responses of Sargassum thunbergii to different concentrations (0, 0.1, 0.5, 1.0 and 5.0 mg/L) of zinc (Zn) and cadmium (Cd) exposure separately were studied for 15 days in laboratory-controlled conditions. The results show that the specific growth rates increased slightly under the lower Zn concentration treatment (0.1 mg/L) at the first 5 d and then decreased gradually, which were significantly reduced with the exposure time in higher Zn concentrations and all Cd treatments compared to respective control, especially for 1.0 and 5.0 mg/L Cd. Chlorophyll a contents showed significant increase in 0.1 mg/L Zn treatment, whereas the gradually reduction were observed in the other three Zn treatments and all Cd treatments. The oxygen evolution rate and respiration rate presented distinct behavior in the Zn-treated samples, but both declined steadily with the exposure time in Cd treatments. The P/R value analyses showed similar variation patterns as chlorophyll a contents. Real-time PCR showed that lower Zn concentration (0.1 mg/L) increased mRNA expression of rbcL gene, whereas higher Zn concentrations and Cd reduced the rbcL expression. Taken together, these findings strongly indicate that Zn and Cd had different effects on S. thunbergii both at the physiological and gene transcription levels, the transcript level of photosynthesis-related gene rbcL can be used as an useful molecular marker of algal growth and environment impacts.