This work resulted from an expedition to the Azores on board of "NTM Creoula" in summer 2005, organized by the Portuguese Navy, the Portuguese Federation for Underwater Activities (FPAS) and National Geographic Portugal. Surface sediment samples were collected from two contrasting sites: Horta Bay, a natural sheltered embayment with an important commercial and recreational port, and D. João de Castro Bank, a shallow seamount with hydrothermal activity and virtually no human impact. Samples were collected respectively by snorkelling and SCUBA diving, and kept cold and in the dark until processing, to prevent cyst germination. Laboratory procedures involved wet sieving of ca. 20ml of sediment per site and concentration by centrifugation using a heavy-liquid, to maximize the recovery of the cyst fraction. Permanent slides were mounted with aliquots of the rich cyst fraction and examined under the light microscope. The presence of cell contents was registered and assumed to be an indicator of recent cyst production. Sediments from Horta Harbour were fine and silty while at D. João de Castro Bank the recovered sediment was almost only volcanic rock and debris. Samples were poor, and a total of 201 cysts belonging to 15 different taxa were recovered. The 2 sites had a similar species richness (S=11) but different trophic and taxa composition. The embayment sample (Horta Harbour) was rich in Protoperidinium and Scrippsiella-like cysts (with no and -like cysts (with no calcareous walls probably due to dissolution) having a balanced proportion of heterotrophic (45%) and photosynthetic (55%) species. By contrast, the seamount sample was largely dominated by autotrophs (93%), mainly Protoceratium reticulatum, Spiniferites and Scrippsiella. The percentage of cysts and The percentage of cysts with cell content in Horta Harbour was 36%, against 67% for D. João de Castro Bank. These differences reflect the contrasting nature of the two sites. Horta Harbour lies inside a natural sedimentary basin where cyst production, transport and sedimentation are integrated in space and time. By contrast, due to erosion and re-suspension, the cyst community in D. João de Castro Bank reflects mainly recent cyst production. Wall et al. (1977) studied a sample from a harbour in the Azores (Ponta Delgada, São Miguel Island) and reported calcareous cysts (Scrippsiella trochoidea) as dominant. These authors observed ) as dominant. These authors observed Protoceratium reticulatum maximum abundances in maximum abundances in shelf and slope-rise zone sediments. The fact that D. João de Castro Bank was dominated by recently formed cysts of this species suggests that this seamount constitutes an ecological niche which favours coastal-oceanic transition species. This study, although limited in time and space, gives an insight into the dinoflagellate cyst assemblages of the Azores. Further work is needed in this region to better resolve the taxonomy and ecology of this group and determine the ecological role of seamounts.