The summer spatial distribution of the dinoflagellate community along an open coastal sea gradient in the Gulf of Gabes (Tunisia, Eastern Mediterranean Sea), together with environmental factors, were studied. The most dominant families were represented by Gymnodiniaceae (32%), Peridiniaceae (20%), Prorocentraceae (15%), Ceratiaceae (13%) and Ebriaceae (10%). The dinoflagellate community was spatially more concentrated along the coast of the gulf than in the open sea. Eight toxic dinoflagellates were recorded, including Karenia cf. selliformis (37% of total toxic dinoflagellates) which was evenly distributed in both the neritic and open sea areas. Dinocysts contributed 33% of the total motile cells and were more abundant along the coast than in the open sea. This high concentration may be ascribed to nitrogen inputs in the coastal waters of Gabes. The Modified Atlantic Water governed dinoflagellate development in the open sea. The degradation of the water quality due to eutrophication in the Gulf of Gabes may have significant socioeconomic consequences. We suggest that a management framework, similar to that used in freshwater ecosystems, should be developed for the Gulf coast in order to drastically reduce urban interferences.