Ecophysiological studies looking at the combined effects of ocean acidification (OA) and iron (Fe) availability on Southern Ocean (SO) phytoplankton are still limited. To gain a better mechanistic understanding of how the two ecologically important SO phytoplankton groups cope with OA and Fe limitation, we conducted laboratory incubation experiments on the Antarctic cryptophyte Geminigera cryophila and the diatom Pseudo‐nitzschia subcurvata. Geminigera cryophila (CCMP 2564) was isolated from the Southern Ocean and obtained from Matt Johnson's Laboratory of Protistan Ecology at the Woods Hole Oceanography Institute, United States. Pseudo-nitzschia subcurvata was isolated from the Southern Ocean by P. Assmy during Polarstern expedition ANT- XXI/4. Both species were grown at 2°C under different pCO2 (400 vs. 900 μatm) and Fe (0.6 vs. 1.2 nM) conditions. For P. subcurvata, an additional high pCO2 level was applied (1400 μatm). For both species, growth, photophysiology, cellular quotas of particulate organic carbon, trace metals and pigments were assessed. Our study reveals that Fe limitation was detrimental for the growth of G. cryophila and suppressed the positive OA effect. The diatom was efficient in coping with low Fe, but was stressed by OA while both factors together strongly impacted its growth. The distinct physiological response of both species to OA and Fe limitation explains their occurrence in the field. Based on our results, Fe availability is an important modulator of OA effects on SO phytoplankton, with different implications on the occurrence of cryptophytes and diatoms in the future.