Abstract. The present work aims at understanding the importance of Brzezinski–Redfield ratio (modified Redfield ratio) as a determinant of natural phytoplankton community composition in a mangrove ecosystem. Even though this ecoregion has been reported to be mostly eutrophic, localised and anthropogenic influences often result in habitat variability especially with regard to nutrient concentrations at different parts of this ecosystem. Phytoplankton, an important sentinel in aquatic ecosystems may respond differently to such alterations in habitat thereby bringing about significant changes in the community composition. Results show that even though habitat variability does exist at our study area and varied on a spatial and temporal scale, the nutrient concentrations were intricately balanced that never became limited and complemented well with the concept of modified Redfield ratio. However, an integrative approach to study phytoplankton community involving microscopy and rbcL clone library and sequencing approach revealed that it was the functional traits of individual phytoplankton taxa that determined the phytoplankton community composition rather than the nutrient concentrations of the study area. Hence we conclude that the recent concept of functional traits and elemental stoichiometry does not remain restricted to controlled environment of experimental studies only but occur in natural mangrove habitat.