Harmful dinoflagellate cysts refer to cysts derived from dinoflagellates that can produce toxins and (or) cause harmful dinoflagellate blooms. So far, 18 species in 10 genera have been recorded along coasts of China seas, accounting for three quarters of the total number of harmful dinoflagellate cysts globally. These harmful dinoflagellate cysts are widely distributed along Chinese coasts. Harmful dinoflagellate cysts largely threaten marine ecosystems, aquaculture industries and even human health. Consequently, the study of diversity and distributions of harmful dinoflagellate cysts has become a hotspot in marine biology and ecology. The identification of harmful dinoflagellate cysts is crucial for sea food safety inspection and prediction of harmful dinoflagellate blooms. However, accurate identification represents a big challenge, mainly owing to limited available morphological features of harmful dinoflagellate cysts. Here we review research progress on harmful dinoflagellate cysts on Chinese coasts, including their negative impacts, diversity and geographical distributions, and species identification of harmful dinofagellate cysts. In addition, we suggest that it is nececarry to ultilize multiple methods including those based on morphology and molecular biology, as well as methods based on toxicology and reproductive biology, to accurately identify harmful dinoflagellate cysts.