Although iron (Fe) availability sets primarily the rate of phytoplankton growth and primary and export production in the Southern Ocean, other environmental factors, most significantly light, also affect productivity. Due to wind-induced vertical mixing, the total irradiance dose can be reduced, but exposing phytoplankton also to periods of excessive irradiance when residing near the surface. As these dynamic alterations between low and high irradiance in low Fe-waters are important drivers of species distribution, we investigated the effects of light (20, 200 and 500 μmol photons m−2 s−1) in combination with low and high Fe availability (0.4 and 2 nM Fe) on the physiology of the two ecologically relevant species Chaetoceros debilis and Phaeocystis antarctica. Fe-limited cells of P. antarctica displayed similar high growth rates at all irradiances. In comparison, Fe-limited C. debilis cells grew much slower under low and medium irradiance and were unable to grow at the highest irradiance. Compared to C. debilis Fe-limited P. antarctica cells fixed more particulate organic carbon at all irradiances. When exposed to short-term excessive irradiances C. debilis could cope better than P. antarctica under low Fe conditions, but this was at the expense of lowered carbon production. Overall, our results show that P. antarctica was more tolerant to changes in the availability of Fe and light, providing it a competitive advantage under a dynamic light regime in Fe-deficient waters.