This is the first study on the dinoflagellate cysts in Algerian waters and in Mellah Lagoon (South Western Mediterranean), 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 heterogeneous. 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 \textless 0.05), organic matter (r = 0.70; p \textless 0.05), water content (r = 0.71; p \textless 0.05), and the fine fraction of sediment (r = 0.74; p \textless 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 Gymnodinium catenatum 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 program to prevent a potential human intoxication due to the consumption of contaminated sea products by these potent neurotoxins.