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Impacts of ocean acidification (OA) on noncalcifying organisms and the possibly responsible mechanism have aroused great research interests with the intensification of global warming. The present study focused on a noxious, noncalcifying, bloom-forming dinoflagellate, <i>Karenia mikimotoi</i> (<i>K. mikimotoi</i>), and its variation of growth patterns exposed to different periods of seawater acidification with stressing gradients was discussed. The dinoflagellates under short-time acidifying stress (2d) with different levels of CO₂ presented significant growth inhibition (<i>p</i> < 0.05). The cell cycle was obviously inhibited at S phase, and the photosynthetic carbon fixation was also greatly suppressed (<i>p</i> < 0.05). Apoptosis was observed and the apoptotic rate increased with the increment of <i>p</i>CO₂. Similar tendencies were observed in the key components of mitochondrial apoptotic pathway (the mitochondrial membrane potential (MMP), Caspase-3 and -9, and Bax/Bcl-2 ratio). However, under prolonged stressing time (8 d and 15 d), the growth of dinoflagellates was recovered or even stimulated, the photosynthetic carbon fixation was significantly increased (<i>p</i> < 0.05), the cell cycle of division presented little difference with those in the control, and no apoptosis was observed (<i>p</i> > 0.05). Besides, acidification adjusted by HCl addition and CO₂ enrichment resulted in different growth performances, while the latter had a more negative impact. The results of present study indicated that (1) the short-time exposure to acidified seawater led to reduced growth performance via inducing apoptosis, blocking of cell cycle, and the alteration in photosynthetic carbon fixation. (2) <i>K. mikimotoi</i> had undergone adaptive changes under long-term exposure to CO₂ induced seawater acidification. This further demonstrated that <i>K. mikimotoi</i> has strong adaptability in the face of seawater acidification, and this may be one of the reasons for the frequent outbreak of red tide. (3) Ions that dissociated by the dissolved CO₂, instead of H⁺ itself, were more important for the impacts induced by the acidification. This work thus provides a new perspective and a possible explanation for the dominance of <i>K. mikimotoi</i> during the occurrence of HABs.