The paper describes the community composition of phytoplankton in the eastern Arabian Sea (EAS) during winter monsoon (WM, January–February 2018), encompassing the entire eastern part of the Arabian Sea basin (~6–22°N and 77–67°E) with high-resolution sampling (7 transects, 56 sites), from coastal to offshore regions. The phytoplankton pigment concentrations estimated by high-performance liquid chromatography were interpreted using ‘CHEMTAX’ (Mackey et al., 1996) to determine relative abundance and contribution of phytoplankton functional groups at the class level. A distinct spatial heterogeneity was observed in the distribution of phytoplankton groups in the coastal and offshore regions of the northern as well as southern part of the EAS. The basin-scale column integrated chlorophyll a (Chl a) concentration in the upper 100 m was higher (16–118 mg m−2) in the northeastern Arabian Sea (NEAS) as against 9–79 mg m−2 in the southeastern Arabian Sea (SEAS). The chromatographic analysis revealed the dominance of diatoms in the coastal waters of the EAS basin. A closer evaluation of the hydrodynamics and nutrient chemistry of the offshore regions revealed that entrainment of sub-halocline nutrients into the sunlit water column through convective mixing supported the dominant cyanobacterial population in the NEAS. In the warm oligotrophic waters of the SEAS, the substantially high NH4+ concentration indicates that the dominant prochlorophytes were sustained by the regenerated production. The dominance of large phytoplankton like diatoms indicates a herbivorous control in the food chain in coastal waters of the EAS. Offshore waters are characterised by large proportions of pico-nano plankton along with considerable micro phytoplankton, which suggests a mixotrophic ecosystem. The statistical analysis showed that the silicate (Si/N ratio) concentration played a major role in controlling the diatom abundance in the coastal areas of the north (south) EAS while temperature and salinity together with nutrients structured the phytoplankton assemblage in the offshore waters during WM.