The Changjiang Estuary is the biggest estuary in China and is strongly affected by the huge runoff of the Changjiang River as well as other hydrodynamic factors such as upwelling and currents. These comprehensive factors bring large amounts of nutrients which are supplied for high primary production. On the hand, multi-source of nutrient loading also resulte in frequent HAB events in this area.Cyst-formation is an important stage in the life cycle of some marine dinoflagellates, especially when environmental conditions are adverse. Cysts can germinate as soon as environmental condition become favorable. Therefore, cysts play an important ecological role as the source of causative species for recurrent blooms. In order to understand the population dynamics of algal blooms, the surface sediments (10 cm in length) at 19 sites (E121°-127°, N30°-32.5°) were collected from Changjiang Estuary during December, 2006 to February, 2007 to investigate the horizontal and vertical distribution of dinoflagellate cysts. Samples were sonicated and then sieved through 125μm and 20μm metallic screens, and the objective materials were captured for observation. Twenty seven different cyst morpho-types were identified, including 10 autotrophic and 17 heterotrophic species that belong to 6 groups.The ratio of species number for the autotrophic and heterotrophic cysts was 0.70. Species richness in each sample varied from 1 to 15. There were no obvious difference in cyst composition among surface layer, middle layer and bottom layer. The Protoperidinium group was the most dominant group in each layer with an average proportion of 55.2%. The Gonyaulacoid group was the second abundant group, with a mean proportion of 36.1%. Compared to other sea areas, the cysts concentration in the Changjiang Estuary was relatively low. The average density of cysts varied from 0.7 to 89.0 cysts per gram dry weight at each sampling site. The cysts concentrations in Changjiang Estuary, North of Jiangsu, Hangzhou Bay, Zhoushan and the open water was 29.14 per gram dry weight, 19 per gram dry weight, 10.42 per gram dry weight, 30.67 per gram dry weight and 51.08 per gram dry weight respectively. In the vertical direction, the concentration of dinoflagellate cysts was most abundant in the surface layer, and least in the bottom layer. In the surface layer, cyst density varied markedly among stations, ranging from 2 cysts per gram dry weight in sample of M4-13 to 120 cysts per gram dry weight in the sample of M4-11. In longitudinal direction, the cyst concentration increased from station M4-1 to M4-13, decreased at station M4-13, then increased gradually again from C16-3 to C16-9. Alexandrium cysts occurred at the most sampling sites but in low numbers. The maximum concentration of Alexandrium cysts was 40.8 per gram dry weight. They were mainly found in off shore areas, less in numbers in Hangzhou Bay. Other species such as Polykrikos kofoidii, Gonyaulax spinifera complex (Spiniferites mirabilis) and G. spinifera complex (S. cf. ramosus) were also observed. The sediment type is considered as the most important factor of the distribution pattern of dinoflagellate cysts. Water depth, temperature, salinity have a positive correlation with the distribution of cysts while dissolved oxygene has a negative correlation with the distribution of cyst. The distribution of cysts can be used as a good indicator for eutrophication and hypoxia in the Changjiang Estuary.