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Bardawil is a shallow hypersaline lagoon, with salinity ranging between 38.18 and 62.40 PSU. It is a source of good quality fish and wildlife. The phytoplankton was evaluated seasonally (summer 2013 to spring 2014), at 12 stations. A total of 186 taxa from 95 genera and seven classes, namely, Bacillariophyceae, Dinophyceae, Chlorophyceae, Cyanobacteria, Euglenophyceae, Rhodophyceae and Chrysophyceae were recorded. The phytoplankton community was dominated by Bacillariophyceae followed by Dinophyceae. The Shannon-Wiener Diversity Index (1.75-3.30) classified Bardawil Lagoon as being a not stressed environment. Differences in the phytoplankton community structure and abundance between previous results and the present study showed significant changes with the change in salinity. Seasonal differences in the quantitative and qualitative composition of the phytoplankton communities in the different sites were marked. The phytoplankton annual succession was characterized. No sign of eutrophication was observed, and most of the dinoflagellate species detected have been described as harmful or able to occur at high biomass. The study showed that Bardawil water is still oligotrophic, free of contaminants, so we suggest the need to add fertilizers to accelerate the production of natural food organisms to increase fish and crustacean production. Before the addition of any fertilizer, it must dig two or three canals to facilitate exchange of water between the Mediterranean Sea and the lagoon to prevent undesirable harmful algae bloom.