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Abstract: A qualitative and semi-quantitative study of recent dinoflagellate cysts has been undertaken in the NW part of Aegean Sea, Thermaikos Gulf (Eastern Mediteranean), before (September 2001), during (October 2001) and after 120 days (February 2002) of intensive trawling activities. This is the first survey of recent dinoflagellate cysts from Greek marine coastal environments. Sediment samples were collected with a corer and the vertical distribution of the cysts was studied at five different layers, from 0 to 10cm. Dinoflagellate cysts were both abundant and diverse. Cysts were found over the whole sampling area and periods, with concentrations ranging between 247–3202cystscm−3. Thirty-six cyst types were encountered, of which 32 were identified to species level, representing 12 genera. It seems that significant local resuspension, related to the onset of the trawling period and stirring up of the sediment, contributed to mixing of the upper layers, resulting to more homogenous cyst profiles in the sediment. Viable cysts constituted 16–60% of the total cyst abundance. The abundance peaks of viable cysts within the subsurface sediment layers, observed during the undisturbed period, disappeared during October. In February, the reduction of cyst concentration was associated to a loss of viable cysts, whilst the ratio of viable/empty cysts ranged between 0.30 and 0.67. The abundance of the different dinoflagellate species, in their active form, was monitored in order to detect any relationship between the concentration of cysts in the top 10cm of sediment and blooms of algae in the water column. Cysts of potentially toxic species, causing Paralitic Shellfish Poisoning (PSP), such as Alexandrium cf. tamarense, A. cf. affine, A. cf. minutum, as well as Gymnodinium catenatum, were detected in the cyst survey. [Copyright &y& Elsevier]