A sediment trap study was conducted in the Gulf of Venice, north-western Adriatic Sea, from April to December 2005 to assess relationships between planktonic dinoflagellates and cyst production. Every month, CTD profiles and discrete samplings for phytoplankton, nutrients and particulate matter were conducted. Cyst fluxes spanned from 90 to 127,600 cysts m-2 d-1 and major peaks were due to a small cyst attributed to cf. Biecheleria and to calcareous cysts of Scrippsiella trochoidea. A good correspondence between cyst fluxes in sediment traps and the presence of the corresponding vegetative cells in the water column was detected for Lingulodinium polyedrum, and species of the genera Spiniferites,Gonyaulax and Protoperidinium. A PCR method applied to surface sediment samples allowed the identification of a number of potentially harmful dinoflagellate cysts (Alexandrium minutum, A. tamutum, A. taylorii, Lingulodinium polyedrum and Protoceratium reticulatum).