Many blooms of the toxic dinoflagellate Alexandrium minutum have been recorded since 1990 in the Gulf of Gabes (southwestern Mediterranean Sea). To understand the determining factors of bloom formation, we studied the distribution of A. minutum in relation to environmental factors in samples taken at shallow sandy (<1 m) beach stations and a lagoon between 1997 and 2006. This was accompanied by laboratory experiments to identify A. minutum. The species forms harmful algal blooms (HABs) in stations subjected to anthropogenic eutrophication and in confined lagoons, living under conditions of varying salinity which gives it a unique opportunity to broaden its physiological tolerance and increase its colonisation potential. Increases in phosphorus appear to be more important than nitrogen or temperature in the control of A. minutum. The stations sampled all along the coast present specific hydrographic properties (shallowness, turbulence) suggesting that factors other than temperature and nutrients influence Alexandrium distribution, the exception being Boughrara Lagoon where the species developed in accordance with published data. Our findings and their interpretations indicate that the mechanism of the sudden A. minutum blooms along the nearshore of the Gulf of Gabes was complex and differed from that of true coastal ecosystems.