The ocean acts as a major sink for anthropogenic CO2 emissions, which causes seawater pH to decline (Ocean Acidification, OA) and it has been shown, that Southern Ocean Pseudo-nitzschia spp. vanish from natural phytoplankton communities, when incubated under OA. To gain a better understanding of the physiological mechanisms that make this genus susceptible to OA, two species, P. turgiduloides and P. turgidula were cultured under three levels of pCO2 (350 μatm (LC); 1000 μatm (MC); 1300 μatm (HC)) to assess the effect on growth rates, particulate organic carbon production and photophysiology. Growth of both species strongly declined with increasing pCO2, the number of non-viable cells increased and some viable cells showed morphological malformations of frustules. Electron transport rates were downregulated to prevent overconsumption of electrons in upstream processes like carbon fixation and thereby a limitation of ATP production. Moreover, the increase of NPQ in both species demonstrates active regulation by dissipation of energy in response to OA. These combined effects were already evident at MC for P. turgidula whereas for P. turgiduloides they only showed under HC, indicating that the former species was susceptible to lower pCO2. Neither photosynthetic efficiency, nor connectivity (i.e., energy transfer between photosystem II), or reoxidation time of the primary electron acceptor were impaired by increasing pCO2 in the two tested species, providing further evidence of active regulation rather than damage to the photosystems. The two investigated diatoms are common in open ocean environments and are thus not exposed to natural fluctuations in seawater pH as they would be in coastal environments. This could be the reason why P. turgiduloides and P. turgidula are less resilient to OA.