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Abstract The Bay of Bengal (BoB) is a 2,600,000 km²expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients—which have low temperature variation (27–29°C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters,Prochlorococcusaveraged 11.7 ± 4.4 × 10⁴ cells ml⁻¹, predominantly HLII, whereas LLII and ‘rare’ ecotypes, HLVI and LLVII, dominated in the SCM.Synechococcusaveraged 8.4 ± 2.3 × 10⁴ cells ml⁻¹in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites,OstreococcusClade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea‐influenced high salinity (southerly; prasinophytes) to freshwater‐influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyteMicromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 × 10⁴ cells ml⁻¹, surface) where a novelOstreococcuswas revealed, named hereOstreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto ‘rare’ picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change.