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The dinoflagellate genus <i>Scrippsiella</i> is a common member of phytoplankton and their cysts are also frequently reported in coastal sediments worldwide. However, the diversity <i>of Scrippsiella</i> in Korean waters has not been fully investigated. Here, several isolates of <i>Scrippsiella precaria</i> collected from Korean waters and germinated from resting cysts were examined using light and scanning electron microscopy. The resting cysts were characterized by pointed calcareous spines and one or two red accumulation bodies, and the archeopyle was mesoepicystal, representing the loss of 2–4′ and 1–3a paraplates. Rounded resting cysts were found in culture, and an increase in spine length was observed until 8 days of development. Korean isolates of <i>S. precaria</i> had the plate formula of Po, X, 4′, 3a, 7″, 6C, 4S, 5‴, 2⁗. There were differences in the cell size and location of the red body between Korean isolates and previously described cells of <i>S. precaria</i>. In addition, the Korean isolates of <i>S. precaria</i> had two types of the 5″ plate that either contacted the 2a plate or not. Molecular phylogeny based on internal transcribed spacer (ITS) and large subunit (LSU) rDNA sequences revealed that the Korean isolates were nested within the subclade of PRE (<i>S. precaria</i> and related species) in the clade of <i>Scrippsiella</i> sensu lato, and that the PRE subclade had two ribotypes: ribotype 1 consisting of the isolates from Korea, China, and Australia, and ribotype 2 consisting of the isolates from Italy and Greece. Lineages between isolates of ribotype 1 were likely to be related to the dispersal by ocean currents and ballast waters from international shipping, and the two types of spine shapes and locations of the 5″ plates may be a distinct feature for ribotype 1.