This study examined the relationship between dinoflagellate cysts and vegetative cells, to a certain extent, by conducting a germination experiment on dinoflagellate cysts collected from a sediment trap and surface sediment. The germination experiment showed that 56.8%, 25 of the 44 species of dinoflagellate cysts seen in the sediment trap, germinated, which confirmed the relationship between cysts and vegetative cells. The germination experiment also found that Votadinium carvum showed different forms of vegetative cells in all three forms of cysts, which required an accurate identification of the species through a genetic analysis. Furthermore, the species known to be the cyst of Cochlodinium polykrikoides was determined to be Cochlodinium sp., and the cysts of C. polykrikoides did not appear.