The consequences of ocean acidification (OA) on marine phytoplankton have been intensively studied ranging from cellular to ecosystem level. These investigations, however, almost exclusively focused on coccolithophores and diatoms. Dinoflagellates also represent an important group of phytoplankton, featuring the photosynthetic key enzyme type II RubisCO, with very low affinities for its substrate CO2. Hence, we expect this group to be particularly sensitive to changes in CO2 concentrations. In this study, we therefore investigated the impact of OA on the eco-physiology of two dinoflagellate species, the calcareous Scrippsiella trochoidea and the toxic Alexandrium tamarense, by using dilute batch incubations over a range of CO2 levels. Our results show that with rising pCO2, growth rates and chlorophyll a contents remained relatively unaltered, but also species-specific differences were observed. For instance, Scrippsiella displayed a strong decrease in organic carbon production, and Alexandrium showed a shift in its toxin profile towards less toxic variants under elevated CO2. To understand these eco-physiological responses, several aspects of inorganic carbon (Ci) acquisition were investigated by means of membrane-inlet mass spectrometry. Both species featured efficient carbon concentrating mechanisms (CCMs), which in Scrippsiella was further facilitated by a high carbonic anhydrase activity. In Scrippsiella, maximum photosynthetic rates increased while Ci affinities decreased. Interestingly, in Alexandrium the opposite response pattern was observed. Our results show that dinoflagellate species have different strategies to adjust their Ci acquisition, which may enable them to keep their growth rates unaffected over a range of CO2 levels.