This is the first study on the dinoflagellate cysts inAlgerianwaters and in Mellah Lagoon (SouthWesternMediterranean), located  within a protected reserve. In total, 42 species of dinocysts belonging to 7 orders, 12 families and 23 genera, were identified in the  26 superficial sediment samples from Mellah Lagoon. The distribution of dinocysts in the sediment of this lagoon is heteroge- neous. Indeed, their abundance oscillates between 1 and 315 cysts g−1 dry sediment (DS). Cyst morphotype assemblages were dominated by a few numbers of species: Alexandrium minutum (15.87%), Gonyaulax verior (9.81%), Protoperidinium spp.  (7.74%), Alexandrium affine (7.05%), Scrippsiella trochoidea (6.67%), and Alexandrium pseudogonyaulax (6.19%). There is a  positive correlation between the density of cysts and the depth (r = 0.61; p < 0.05), organic matter (r = 0.70; p < 0.05), water  content (r = 0.71; p < 0.05), and the fine fraction of sediment (r = 0.74; p < 0.05). Surprisingly, although the Mellah Lagoon is  almost semi-closed, it holds an important specific richness in dinocysts (42 species) higher than others observed in Mediterranean  lagoons. However, cyst abundances are low compared to other lagoons in the Mediterranean Sea. Finally, the presence of  dinocysts of Alexandrium catenella/tamarense, A. minutum, and Gymnodiniumcatenatum associated to paralytic shellfish toxins,  A. pseudogonyaulax which produces goniodomin A, also Protoceratium reticulatum and Gonyaulax spinifera complex which  produce yessotoxins, needs to implement a monitoring programto prevent a potential human intoxication due to the consumption of contaminated sea products by these potent neurotoxins.