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The Gulf of Mannar (GoM) and the Palk Bay (PB) are two least studied marine environments located between India and Sri Lanka. Exceptionally high chlorophyll a concentration in the GoM and the PB during the Northeast Monsoon (November-February) is a consistent feature in satellite imageries, which has been attributed to the intrusion of the Bay of Bengal (BoB) waters. The analyses of the Moderate Resolution Imaging Spectroradiometer (MODIS) and field chlorophyll data collected from 30 locations in the Indian sector of the GoM and the PB in January 2011 showed significant overestimations in the satellite data. This error was much higher in the PB (60-80 %) as compared to the GoM (18-28 %). The multivariate analyses evidenced that the exceptionally high satellite chlorophyll in the PB is contributed largely by turbidity, colored dissolved organic matter (CDOM), and bottom reflectance. The paper cautions that though MODIS is superior in estimating chlorophyll a in optically complex waters, there are still chances of overestimations in regions like the PB.