The dinoflagellate genus Karenia is known for recurrent harmful blooms worldwide. However, species diversity of the genus is generally overlooked owing to the difficulty of identifying small unarmored dinoflagellates. We have established four clonal cultures of Karenia longicanalis isolated from the type locality, Hong Kong harbor (strain HK01) and other three locations along the Chinese coasts (strains YB01, DT01, and NJ01). The morphology of the strain was studied by light and scanning electron microscopy (LM and SEM) and the pigment composition analyzed by high-performance liquid chromatography. We provide the first molecular data of K. longicanalis based on the large subunit (LSU) rRNA gene sequence and internal transcribed spacer (ITS). The four strains showed identical LSU rDNA sequences with a similarity of 99.4% to the holotype of Karenia umbella (strain KUTN05) from Australia. In the ITS phylogeny, the sequence of K. umbella branched between the Chinese strains of K. longicanalis. A careful comparison of the morphology of K. longicanalis and K. umbella reveals the similarity in the diagnostic characters. Differences may appear due to the sample treatment for SEM. We conclude that K. umbella is a junior synonym of K. longicanalis.