Dinoflagellate cysts play an essential role in the initiation, recurrence and geographical expansion of harmful algal blooms (HABs). The horizontal distribution and abundance of dinoflagellate cysts in marine sediments provide essential information in giving early warnings of the presence of toxic species and possible continuing recurrence of HABs in a given area. This research carried out in the waters of Jakarta Bay. Sediment samples collected from thirteen sampling stations using TFO gravity corer 2.1 cm diameter from sediment thickness 0-4 cm. The results showed that resting cysts belong to Gonyaulax, Alexandrium, Scrippsiella, Protoperidinium, Gymnodinium, Gyrodinium. Two of them, namely Gymnodinium sp and Alexandrium sp, known as toxic species. Cysts in the sediment thickness 0-4 cm mainly dominated by the group of Gonyaulax (Gonyaulacoid). Cyst abundance in the sediment depth-layer 0-2 cm is higher than in depth-layer 2-4 cm. The number of dino-cysts in sediment layer 0-2 cm ranged from 2.984 – 22.298 cysts cm−3 while in the layer 2-4 cm the amount varies from 1.063 – 8.132 cysts cm−3 of wet sediment. The result revealed that dino-cyst abundance is higher in the deposit collected from locations near to the coast. The assemblages of dinoflagellate resting cysts seemed to have a relation with some hydrological parameters.