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Abstract The Indian Sector of the Southern Ocean (ISSO) is a key region for global biogeochemical cycling, where strong frontal systems regulate nutrient supply and ecosystem structure. During two austral summer expeditions (2018 and 2020), we examined phytoplankton and zooplankton communities across the Subtropical Front (STF), Subantarctic Front (SAF), Polar Front (PF), and south of the Polar Front (SPF) using hydrography, nutrients, HPLC–CHEMTAX pigments, microscopic cell counts, taxon‐resolved carbon biomass, and zooplankton abundances. Environmental gradients were pronounced: STF surface waters were warm (12–16°C) and saline (~ 35), with low nitrate and silicate, whereas PF/SPF waters were cooler (0–3°C), fresher, and nutrient‐rich, with silicate up to 49 μ M. These gradients structured phytoplankton composition: cryptophytes contributed 40–50% of chlorophyll‐ a in STF, while dinoflagellates ( Gyrodinium sp.) reached ~ 1400 cells L −1 , contributing ~ 1.0 μ g C L −1 . Polar Front and SPF were dominated by diatoms ( Fragilariopsis sp., Chaetoceros sp., Thalassiosira sp.), contributing 45–55% of chlorophyll‐ a and up to 1.7 μ g C L −1 . Zooplankton co‐varied with phytoplankton, with calanoid copepods increasing from ~ 110 ind. m −3 in PF (2018) to ~ 756 ind. m −3 in 2020, coinciding with higher diatom biomass in the same frontal zones. Correlations confirmed associations, with cryptophytes positively linked to temperature and negatively to nitrate and silicate, while diatoms were associated with cooler, nutrient‐rich waters. These findings show that gradients in temperature, salinity, and nutrients structure phytoplankton composition and carbon biomass, which in turn co‐vary with zooplankton. This study provides a quantitative assessment of interannual variability in the ISSO and highlights the critical role of frontal systems in modulating Southern Ocean carbon cycling.