The genetic diversity of marine benthic dinoflagellate strains morphologically identified as Moestrupia oblonga from the coastal areas of Okinawa Island, Japan, were investigated. All strains shared similar morphologies, such as unarmored cells with a rice grain-like shape, the cingulum displacing about one third of the body length, a distinctive ventral flange, and a conspicuous central pyrenoid, while the nucleus was positioned in the hypocone, conforming to the general morphology of M. oblonga LarsenandPatterson Hansen and Daugbjerg from Tenerife, Canary Island, Spain. Molecular phylogenetic analyses based on LSU rDNA D1-D3 and the concatenated dataset of SSU-ITS1-5.8S-ITS2-LSU rDNA sequences indicated that all strains are monophyletic, but separated into three genetically distinct clades; namely, Clade A, B, and C. Intraclade sequence divergence in the respective clades was less than 0.3 % for all molecular markers, excluding the ITS1-5.8S rDNA-ITS2 region of Clade B and Clade C that showed sequence divergence of 0.7 % and 1.75 % among its members, respectively. The mean interclade divergences between clades were about 1.2–3.7 % in SSU rDNA, but reached 18–26 % and 6.3–9.7 % for nucleotides in ITS and LSU rDNA sequences, respectively. Despite the link between the three Okinawan clades and M. oblonga JF272764 from Spain showing close affinity in LSU rDNA D1-D3 phylogeny, they diverged about 7.5–12 % regarding base pairs from this sole representative of the genus. Moreover, the formation of these clades was somewhat consistent with morphological differentiation based on cell sizes, indicating that these clades may represent three pseudo-cryptic species in the genus, discreet from M. oblonga from Tenerife, Spain. This study reveals that the genus Moestrupia is much more complex than previous reports have suggested.