Ecology and trophic preference of picoplankton and nanoplankton in the Gulf of Mannar and the Palk Bay, southeast coast of India

► The ecology of smaller plankton components (< 20 mm) in the Gulf of Mannar (GoM) and Palk Bay (PB) is presented. ► The physical barriers located between the GoM and PB inhibits the flow of surface currents. ► The currents during the northeast monsoon period carry low saline Bay of Bengal waters into the PB. ► Flow cytometry and fluorescence microscopy shows differences in distribution of plankton in the GoM and PB. ► The relative tropic preference of various plankton components in the GoM and Palk Bay has been estimated.