This dataset comprises the count data of organic-walled dinoflagellate cysts that were collected by the upper sediment trap on mooring CBi located offshore Cap Blanc, Mauritania between June 2003 and March 2020. The mooring coordinates varied between 20°44.9' - 20°45.7'N and 18°41.9' - 18°42.7'W at water depths between 1249 - 1364 m. The trap had a 0.5 m²opening aperture and material was collected at a 3 to 22 days resolution. In every sampling cup, the material was pre-fixed with HgCl2. Variation in the cyst flux and association composition provided insight into inter-annual to decadal natural and anthropogenic induced changes in the local upper water ecosystem and environment in this region that is characterized by year-round upwelling.