The Southern Ocean (SO) is a net sink for atmospheric CO2 whereby the photosynthetic activity of phytoplankton and sequestration of organic carbon (biological pump) plays an important role. Global climate change will tremendously influence the dynamics of environmental conditions for the phytoplankton community, and the phytoplankton will have to acclimate to a combination of changes of e.g. water temperature, salinity, pH, and nutrient supply. The efficiency of the biological pump is not only determined by the photosynthetic activity but also by the extent of respiratory carbon losses of phytoplankton cells. Thus, the present study investigated the effect of different temperature and salinity combinations on the ratio of gross photosynthesis to respiration (rGP/R) in two representative phytoplankton species of the SO. In the comparison of phytoplankton grown at 1 and 4°C the rGP/R decreased from 11.5 to 7.7 in Chaetoceros sp., from 9.1 to 3.2 in Phaeocystis antarctica strain 109, and from 12.4 to 7.0 in P. antarctica strain 764, respectively. The decrease of rGP/R was primarily dependent on temperature whereas salinity was only of minor importance. Moreover, the different rGP/R at 1 and 4°C were caused by changes of temperature-dependent respiration rates but were independent of changes of photosynthetic rates. For further interpretation, net primary production (NPP) was calculated for different seasonal conditions in the SO with specific combinations of irradiance, temperature, and salinity. Whereas, maximum photosynthetic rates significantly correlated with calculated NPP under experimental 'Spring', 'Summer', and 'Autumn' conditions, there was no correlation between rGP/R and the respective values of NPP. The study revealed species-specific differences in the acclimation to temperature and salinity changes that could be linked to their different original habitats.