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Phytoplankton composition plays a major role in biogeochemical cycles of the ocean. The intensity of carbon fixation and export is strongly dependent on the phytoplankton community. Yet, the contribution of different types of phytoplankton to the total production on various communities is still poorly understood in the Indian Ocean sector of Southern Ocean (SO). Therefore the variability of chlorophyll-a (Chl-a) and diatoms in the frontal ecosystems of the Indian sector of SO have been investigated along with the sea surface temperature (SST), sea surface wind (SSW), photosynthetically active radiation (PAR), and nutrients datasets for the period of 1998–2012. Combined analysis of in-situ, model and satellite observations indicate that the variability of Chl-a and diatoms were primarily influenced by light and wind. The Chl-a was higher at the sub-Antarctic front (SAF) followed by the sub-tropical front (STF) and the polar front (PF). The diatom concentration was higher at the SAF followed by the PF and STF. Maximum concentration of Chl-a and diatoms commonly observed at the SAF region are probably due to the moderate PAR, SST and wind. Dominance of diatoms at the PF may be attributed to their adaptability for low light conditions. The results from this study in the frontal ecosystems would help to understand the biogeochemical cycle of the Indian sector of the SO.