Light and iron levels control bulk primary productivity in the Southern Ocean but their influence on the niche partitioning by co-occurring taxa in the Southern Ocean remains elusive. We used metatranscriptome analyses of a Ross Sea polynya bloom contributed by multiple phytoplankton species to dissect algal acclimation to light and iron levels. Co-occurring algae had functional expression profiles dictated by taxonomy rather than environmental variations. Despite important functional differences, they shared a similar environmental status (low light and low iron condition) in the bloom and key acclimation responses to light and iron regimes. Yet, the overall environmental transcriptomic responses greatly varied between algae: Pseudo-Nitzschia, Chaetoceros, Proboscia and Phaeocystis responded mostly to iron addition while Thalassiosira and Fragiliariopsis were mostly influenced by light. The differences in acclimation among co-occurring algae (including within diatom species) are inconsistent with phylogenetic distances and challenge the light-centric model of algal niche establishments for this remote ocean. They indicate that iron and light govern not only productivity but also the phytoplankton community composition of this highly productive polynya.