The presence of zinc (Zn), a vital element for algal physiological functions, coupled with the silicification of diatoms implies that it plays an integral role in the carbon and silicon cycles of the sea. In this study, we examined the effects of different pCO2 and Zn levels on growth rate, elemental compositions and silicification by Thalassiosira weissflogii. The results showed that under normal pCO2 (400 μatm), cultures of T. weissflogii were depressed for growth rate and silica incorporation rate, but encouraged for cellular silicon content, Si/C, Si/N, and sinking rate when Zn deficient (0.3 pmol L− 1 ). However, cellular silicon and sinking rate of Zn-deficient and Zn-replete (25 pmol L− 1 ) T. weissflogii were decreased and increased at higher pCO2 (800 μatm), respectively. Thus, acidification may affect diatoms significantly differently depending on the Zn levels of the ocean and then alter the biochemical cycling of carbon and silica.