The composition of phytoplankton communities plays a major role in the efficiency of the biological carbon pump and energy transfer to higher trophic levels. Phytoplankton community composition can be significantly affected by changes in environmental conditions. We investigated the effect of increased pCO2 and light intensity on natural communities from two Southern Ocean water masses, the Subtropical Frontal Zone (STFZ) and Subantarctic Surface Waters (SASW). The community in both experiments shifted to predominately dinoflagellates under high pCO2 and high light and the community composition was significantly different between both treatments at the end of the incubation. In the STFZ assemblage, the combination of increased light and pCO2 had a small positive effect on diatom, coccolithophores and picoeukaryote abundance at the beginning of the experiment while higher pCO2 alone had no or a negative effect. In the SASW assemblage, the combination of increased light and pCO2 had a negative effect on diatom abundance while lower pH/higher pCO2 alone resulted in an increase in diatom counts compared to the control. Coccolithophores grew only in the control treatment. Our results show that there are taxon-specific and locality specific differences in natural phytoplankton community responses to increased light and pCO2 within low nutrient regions.