Phytoplankton distribution and concentrations of macronutrients and iron were studied in the Polar Frontal Zone (PFZ) and the eastern Weddell Gyre of the Southern Ocean, during austral autumn. HPLC analysis of algal pigments was combined with microscopy observations to assess algal distribution. Patterns of algal distribution were dictated by the frontal systems. Travelling from north to south, four distinctively different algal communities were observed, the composition of which could be explained by variations in nutrients, light climate and grazing pressure. North of the PFZ, low silicate levels (<3 μM) were limiting diatom growth, and the algal community was dominated by prasinophytes. Silicate concentrations increased over the PFZ, which coincided with the dominance of diatoms. South of the PFZ, the open waters of the Weddell Gyre are characterised as a high nutrient low-chlorophyll area. Low iron concentrations (<0.4 nM on average) supported an algal community that was dominated by smaller size algae (<20 μm). Deep wind-mixed layers (>100 m depth) together with low incident irradiance in autumn were likely limiting algal growth. At the Marginal Ice Zone (MIZ), the phytoplankton community consisted mainly of low numbers of flagellates (Chlorophyceae and haptophytes) and high numbers of microzooplankton, indicating phytoplankton control by grazing. The phytoplankton distribution patterns presented here and the relation with potential growth-controlling factors provides more insight in the mechanisms that control carbon fluxes from the atmosphere into the ocean interior.