The sediments of 19 sites (E121°-127°, N30°-32.5°) about 10cm in length were collected from Changjiang River Estuary from December, 2006 to February, 2007. According to the cyst′s morphological character, 5 groups 27 species were identified including 10 autotrophic and 17 heterotrophic species. 9 species were recorded for the first time in China Sea. They were Scrippsiella sp., Scrippsiella crystallina, Pentapharsodinium tyrrhenicum, Scrippsiella sp. 1, Scrippsiella sp.2, Cochlodinium sp. cf. Geminatum, P. sp. 1, P. sp.2 and Gotoius abei. Two toxic species Alexandrium tamarense/A.catenella complex, A.minutum/A.affine complex and three harmful species Polykrikos kofoidii, Gonyaulax spinifera complex (Spiniferites mirabilis) and Gonyaulax Spinifera complex (Spiniferites cf. ramosus) were observed in this survey. The number of species observed in each sampling site varied from 1 to 15，lowest in M4-13 and N11-4, highest in O7-6. The heterotrophic cysts are dominant in the specific composition. 15,15,12,15 and 13 types of dinoflagellate species were indentified in Changjiang Estuary, North of Jiangsu, Hangzhou Bay, Zhoushan and the open water respectively. The morphological characteristics and the species distribution of the cyst are described in detail in this paper. More recorded dinoflagellate cysts will be helpful to understand species composition of dinoflagellate and population dynamics of causative species of HABs in Changjiang River Estuary.