Ceratocorys armata, C. gourretii, and C. horrida have historically been treated as distinct species based on morphology. Both field samples and cultured strains, however, exhibit continuous morphological variation and intergradations between these taxa. Here, strains from Viet Nam, Japan (Pacific Ocean), and France (Mediterranean Sea, Atlantic Ocean) were analyzed using integrated morphomolecular approaches. Cultured strains revealed morphological intergradations from C. horrida to C. armata and from C. armata to C. gourretii. Phylogenetic analysis based on the ITS1-5.8S-ITS2 rDNA region sequences and the SSU (18S) and LSU (28S) nuclear rDNA gene sequences confirmed the genetic identity of these three taxa for these markers. The ITS2 secondary structure comparisons-including C. malayensis from Viet Nam and Malaysia-further supported their conspecificity, while validating C. malayensis as a distinct species. Based on these data, we have proposed to treat them as formae: C. horrida f. horrida, C. horrida f. armata, and C. horrida f. gourretii. Furthermore, our results indicated that C. malayensis strains from Viet Nam are non-toxic. We have also provided morphological descriptions and illustrations of C. bipes and C. magna, two species rarely reported in the Asia-Pacific region, enhancing the taxonomic clarity of the genus.