Phytoplankton indirectly influence the climate, through their role in the ocean biological carbon pump. Hence factors limiting phytoplankton growth directly impact the strength of the biological carbon pump and consequently climate. In the Southern Ocean, the subantarctic zone represents an important carbon sink, yet variables limiting phytoplankton growth are not fully constrained. Co-limitation by iron (Fe) and manganese (Mn) has recently been observed in the coastal and offshore Southern Ocean, but very few studies have focused on the subantarctic zone. In addition, no study has investigated the seasonal variability of Mn (co-)limitation of phytoplankton growth in the Southern Ocean. Using three shipboard bioassay experiments, we evaluated the seasonality of Fe and Mn co-limitation of subantarctic phytoplankton growth, south of Tasmania. We observed a strong seasonal variation in phytoplankton Fe limitation, and that the response of phytoplankton to Mn was subtle and thus readily masked by the responses to Fe. Combined addition of Fe and Mn enhanced carbon uptake of nanoeukaryotes in spring and microeukaryotes in summer while the addition of Mn alone stimulated the growth of picocyanobacteria in autumn. These results suggest the importance of Mn may vary seasonally and its control on phytoplankton growth may be associated with specific taxa.