The bloom-forming dinophyte Alexandrium minutum comprises biogeographic inferred, global and Pacific clades with both toxic and nontoxic strains reported. A. minutum has a wide distribution in the Western Pacific, but to date only a few strains have available DNA sequences. To fully understand its genetic diversity, sampling was undertaken from the Yellow Sea, the East and South China Sea, and five strains of A. minutum and two strains of its sister species, A. tamutum, were established. Their morphology was examined by light and scanning electron microscopy. In addition, sequences were obtained from both large subunit (LSU) ribosomal DNA and/or internal transcribed spacer (ITS) region. Strains of A. minutum are morphologically indistinguishable, characterized by a smaller cell size and a narrow sixth precingular plate. In contrast, A. tamutum has a wider sixth precingular plate. High nucleotide divergences of LSU (D1–D3) rDNA and ITS were revealed amongst strains of A. minutum (10% and 25%, respectively), and A. tamutum (3% and 13%, respectively). Molecular phylogenies based on LSU rDNA and ITS revealed three ribotypes (B–D) of A. minutum, and two ribotypes of A. tamutum in the Western Pacific. Seasonal sampling in the East China Sea to detect A. minutum using the DNA metabarcoding targeting ITS1 region was also performed. Our results showed that the ribotypes B and C of A. minutum co-occurred in the water. Paralytic shellfish toxin (PSTs) of all seven strains was analysed using liquid chromatography with tandem mass spectrometry (LC–MS/MS). PSTs were detected only in A. minutum ribotypes B and C with predominance of gonyautoxins 1/4. Our results suggest high diversity and risk potential of this toxic species in this region.