Harmful algal blooms (HABs) are becoming widely distributed and more frequent, threatening socioecosystems and human health. We determined species composition, abundance and spatial distribution of dinoflagellate cysts in the upper sediment of the Oualidia Lagoon located on the Atlantic coast of Morocco. Sediment samples were collected in 2017 at 51 stations, and environmental parameters were measured together with microphytoplankton abundance. Sediment characteristics including water percentage, organic matter content and grain size were determined. Fourteen dinoflagellate cyst morphotypes were identified, with Lingulodinium polyedrum (50%) and Gonyaulax spinifera (22%) dominating the assemblages. Total cyst densities ranged from 0 to 293 cysts g(-1) dry sediment. Cyst densities were positively correlated with water content and organic matter content and increased with decreasing sediment grain size. We revealed the presence of three neurotoxic dinoflagellate species: Alexandrium minutum, the Alexandrium tamarense species complex, and Gymnodinium catenatum. Numerous cysts had accumulated in the sediment, and, because they are likely responsible for the initiation of HABs in Oualidia Lagoon, they should be monitored.