<jats:p>The dinoflagellate genus Heterocapsa includes several widely distributed and potentially toxic species associated with Harmful Algal Blooms (HABs), particularly affecting the Western Pacific Ocean. To reveal the biodiversity of Heterocapsa in Beibu Gulf, six strains were morphologically characterized using light and scanning electron microscopy, while large subunit rDNA (LSU rDNA) and internal transcribed spacer (ITS) were sequenced for phylogenetic analysis through maximum likelihood and Bayesian inferences. Two strains (BGERL169, BGERL170) were identified as Heterocapsa philippinensis ribotype I, three (BGERL171-BGERL173) as a new Heterocapsa philippinensis ribotype II, and one strain (BGERL174) as Heterocapsa pseudotriquetra. Cells of H. philippinensis were ovoid to spherical, yellowish-brown, with reticulate chloroplasts, and had a sausage-shaped nucleus positioned longitudinally along the dorsal side of the cell, and the theca was arranged in Po, cp, X, 5′, 3a, 7″, 6c, 5s, 5‴, 2⁗. Additionally, BGERL169 and BGERL171 showed no hemolytic toxicity in rabbit erythrocyte lysis assays. To the best of our knowledge, this research provides the first morphological and phylogenetic analysis of H. philippinensis, including the identification of a new ribotype, as well as the discovery of H. pseudotriquetra in Chinese waters. The findings contribute to the understanding of Heterocapsa species biogeography and toxicity in Chinese waters, offering valuable data for future HAB monitoring in Beibu Gulf.</jats:p>