The resting cyst plays an important role in the life cycle of certain dinoflagellates. Cyst formation is of great significance to populations in terms of perseverance and dispersal. Dinoflagellates producing cysts spend much more time in the sediment than in the water column, and studies on cysts help to uncover dinoflagellate diversity. Cyst diversity and abundance within sediments can reflect the history of overlying dinoflagellates and environmental conditions, and thus serve as a historical record of phytoplankton community and environmental changes. By analyzing the amount and relative proportion of different cysts, the paleo-oceanographical environment can be reconstructed. Here we review recent progress in the study of dinoflagellate cysts within China’s seas. We point out the insufficiency of identifying dinoflagellate cysts based solely on morphological characters, and stress the need to combine results with results of germination experiment. We integrated literature data and provide a checklist of dinoflagellate cyst in China seas: a total of 67 species from 25 genera are listed. Their biological and paleontological names as well as distributional ranges are given. The genus Protoperidinium is most rich with 18 species, followed by Scrippsiella (9), Gonyaulax (7), and Alexandrium (5); other genera contain 1-3 species each. In the present studies in China, species identification based mainly on morphological observations likely result in uncertain taxonomical classification of some species. Finally we discussed fruitful directions for further studies.