In the western Bay of Bengal, some species of heterotrophic dinoflagellates recurrently show symbiotic associations with cyanobacteria (Synechococcus/Synechocystis). The occurrence of these associations is markedly higher during the spring intermonsoon period compared with the summer and winter monsoon. During the spring intermonsoon, strong stratification causes depleted nitrate concentration in the upper water column (upper 60 m water column had <0.01 µM), possibly favouring the proliferation of cyanobacteria cells. During this period, dissolved oxygen concentration in the surface waters (upper 50 m) of the Bay of Bengal were higher than other seasons. The higher oxygen concentrations could retard the process of nitrogen fixation by inactivating the enzyme involved in nitrogen fixation (nitrogenase). The more frequent occurrence of cyanobacterial cells inside the body of heterotrophic dinoflagellates during the spring intermonsoon may, therefore, be an advantage through exposure to reduced oxygen concentrations. Cyanobacterial cells inside the body of dinoflagellates may be more efficient in nitrogen fixation than their relatives in the surrounding water.