Phytoplankton indirectly influence climate through their role in the ocean biological carbon pump. In the Southern Ocean, the subantarctic zone represents an important carbon sink, yet variables limiting phytoplankton growth are not fully constrained. Using three shipboard bioassay experiments on three separate voyages, we evaluated the seasonality of iron (Fe) and manganese (Mn) co-limitation of subantarctic phytoplankton growth south of Tasmania, Australia. We observed a strong seasonal variation in a phytoplankton Fe limitation signal, with a summer experiment showing the greatest response to Fe additions. An autumn experiment suggested that other factors co-limited phytoplankton growth, likely low silicic acid concentrations. The phytoplankton responses to Mn additions were subtle and readily masked by the responses to Fe. Using flow cytometry, we observed that Mn may influence the growth of some small phytoplankton taxa in late summer/autumn, when they represent an important part of the phytoplankton community. In addition, Mn induced changes in the bulk photophysiology signal of the spring community. These results suggest that the importance of Mn may vary seasonally, and that its control on phytoplankton growth may be associated with specific taxa.