Globally, Earth’s warming climate is evidently driving sea ice variability in high latitude regions. In the Arctic, older and thicker multi-year sea ice is declining and transitioning into younger and more ephemeral first-year sea ice. Whereas in Antarctica, sea ice extent is increasing around the continent, masking strong regional reductions around the Western Antarctic Peninsula. Models predict that sea ice will continue to decline into the 21ˢᵗ Century globally. Reduced sea ice cover is expected to impact marine ecosystem functioning through increased primary productivity at the sea surface and increased flux of organic matter to the seafloor. Seafloor sediments are a critical component of the marine ecosystem as sites of organic matter remineralisation and nutrient regeneration, processes which are driven by microorganisms. Despite their importance, our understanding of sediment biogeochemical processes, their connectivity to the water column and to primary productivity at the surface is limited, particularly in polar regions. This impedes our ability to predict the impacts of climate change on marine ecosystem functioning. This study sampled marine sediments from two strategically chosen sites ~60 km apart in McMurdo Sound, Antarctica, where organic matter concentrations were high due to firstyear ice conditions and productive open ocean source waters (Cape Evans), and low due to multi-year ice and oligotrophic source waters (New Harbour). Using high-throughput 16S rRNA gene amplicon sequencing and sediment geochemistry data (chlorophyll-α, phaeophytin, TOC, TN, δ13C, δ15N) this study compared the structure and composition of the sediment microbial communities at these two contrasting sites. The bacterial richness and evenness (alpha diversity) was comparatively greater in the low organic matter sediments underneath the multi-year ice cover than in the high organic matter sediments underneath first-year ice. Significant site-based compositional differences between the two study sites were found. Compositional differences in the high organic matter sediments were driven by known heterotrophic algal biopolymer degrading taxa Flavobacteriales, Cytophagales, and Verrucomicrobiales, and sulfate-reducing bacteria Desulfobulbales, potentially reflecting a sediment legacy of high algal-derived organic matter flux. Whereas the low organic matter sediment communities were driven by chemoautotrophic taxa Nitrosopumilaeles, Nitrospirales, and Steroidobacterales which are known to be involved in carbon fixation and nitrogen cycling, reflecting the legacy of oligotrophic conditions in these sediments. The marine sediments at New Harbour and Cape Evans were not influenced by wind-blown terrestrial surface sediments from the neighbouring Taylor Valley. Additionally, this study supported the hypothesis that subsurface brine channels from the Taylor Valley could be discharging into McMurdo Sound at New Harbour by detecting low abundances of taxa associated with high saline environments (e.g. Thiohalorhabdales). Overall, the findings from this study suggest that climate driven sea ice reductions and increased organic matter flux may shift sediment communities from autotrophy towards heterotrophy, thus impacting sediment biogeochemistry. This study contributes towards our understanding of marine sediment processes and marine ecosystem functioning. Additionally, this study provides a baseline of understanding of sediment microbial communities in McMurdo Sound which will support future research further examining community functional capabilities. Finally, this study contributes a first report of the direct impacts of climate driven sea ice change on sediment microbial communities in Antarctica.