The Ross Sea, Antarctica, is among the most seasonally productive areas globally, where different classes of phytoplankton, such as diatoms and haptophytes (<em>Phaeocystis antarctica)</em>, play key roles in marine ecosystems and the carbon cycle. Sea ice dynamics strongly influence Ross Sea phytoplankton blooms, yet the effects of recent sea ice changes on bloom composition and productivity remain poorly constrained. Seasonally resolved observational records of past Ross Sea phytoplankton and sea ice variability are too short to understand potential future changes in sea ice extent, phytoplankton productivity and community composition, and the resulting consequences on climate. In this study, we investigated phytoplankton-derived lipid biomarkers (fatty acids, highly branched isoprenoids; HBIs, sterols) and diatom assemblages in six marine sediment core tops and three short sediment cores collected along a north-south transect spanning two seasonally recurring polynyas in McMurdo Sound and Terra Nova Bay, to assess how sea ice dynamics and phytoplankton communities drive biomarker signatures and diatom assemblages archived in sediments. For the core-tops, we find that the proportion of open-ocean diatom species and bacterial fatty acid concentrations in core top samples increases towards the southern end of the transect near McMurdo Sound, which is driven by lower summer sea ice extent, a phytoplankton community dominated by diatoms, and higher summer biomass in McMurdo Sound. In contrast, diatom assemblages shift towards sea ice-associated diatoms in the northern end of the transect, characterised by increased concentrations of sea ice diatom-derived fatty acids, sterols, and HBIs (PIPSO₂₅), driven by greater sea ice concentrations. Similarly, <em>Phaeocystis antarctica</em>-derived fatty acid biomarkers increased towards the northern end of the transect, likely driven by differences in the phytoplankton community. For the short cores, we show that an exponential decrease in the fatty acid biomarker signal in the top ~20 cm of sediment is driven by processes such as bacterial biogenesis. Although phytoplankton-derived fatty acids show little change in community composition over the last 200 years, <em>Fragilariopsis curta</em> and PIPSO₂₅ indicate increasing sea ice extent, accompanied by declining <em>Chaetoceros </em>resting spores and open ocean diatom species in the southwestern Ross Sea. Overall, our records reveal a 200-year increasing sea ice trend, consistent with existing regional sea ice extent reconstructions from ice cores. Overall, biomarkers in the southwestern Ross Sea sediment independently distinguish between pelagic diatoms, <em>P. antarctica</em>, and sea ice-associated diatoms, offering a valuable tool for developing decadal resolution records of sea ice and phytoplankton community changes.