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In order to understand the distribution of dinoflagellate cysts, surface sediments were collected from 15 stations in Changjiang River Estuary from 122°E to 123.5°E and from 29°N to 32°N in four cruises from May 2002 to February 2003. In the present study, 38 different cyst morphotypes representing 21 genera and 6 groups were identified, while 1 type was not identified into genus level. Species number and cell density of dinoflagellate cysts ranged from 10 to 25 species and from 12 to 587 per gram of dry weight, respectively. There were no obvious differences in cyst composition and density among seasons. However, the highest cyst species number and density were recorded in summer and winter, respectively. Cysts of heterotrophic dinoflagellates, which held 55.7% of the overall cyst density averagely, dominated cyst assemblages. Cyst density and species number increased from the west to the east, from the north to the south within the study area. Cysts of toxic dinoflagellatesAlexandrium catenellaandAlexandrium tamarensecomplex distributed widely and were observed in almost all stations, with the maximum cell density of 81 per gram of dry weight. [ABSTRACT FROM AUTHOR]