The dinoflagellate genus Heterocapsa includes a lot of potential harmful species but its diversity and biogeography is rarely reported in China. Heterocapsa niei (SIO-H3) was firstly reported in Chinese waters in this study. Its morphological characters were examined by light microscopy, scanning electron microscopy and transmission electron microscopy. Cell shape was peanut-like with plate formula of Po, cp, 5', 3a, 7", 6c, 4s, 5''', 2"". Cell size was 14.3-18.2 μm in length and 8.4-10.9 μm in width. The ratio of length to width ranged from 1.3 to 2.2 with an average of 1.7. Width of epitheca (8.4-10.9 μm) was almost equal to that of hypotheca (9.0-10.9 μm). There were three subcentral uprights on the surface of basal plate of body scale. The nucleus was ellipsoid and located in the hypotheca. Additionally, molecular phylogeny based on internal transcribed spacer (ITS) sequence showed that the isolated strain (SIO-H3) and H. niei (JN020158) were in the same clade with supports of 99% and 97% bootstrap values (1000 replicates) by neighbor-joining and maximum likelihood methods, respectively. The pairwise distance was only 0.004 between them. This report will enrich our knowledge of the geographic distribution of Heterocapsa in China.