In the dinophyte genus Ostreopsis, seven out of 11 described species are known to produce various toxic compounds that were characterized in the palytoxins family. Species in the genus shared identical thecal plate patterns but differed in size, shape, and thecal plate ornamentation. Two species, O. cf. ovata and O. siamensis, have been reported from the Western Pacific, but information on toxin production is scarce. Here, we established nine strains of Ostreopsis from six localities in the South China Sea (SCS), covering the Gulf of Thailand, northern SCS (Hainan Island, Beibu Bay), and southern SCS (Peninsular Malaysia). Their morphology was examined by light and electron microscopy and the molecular phylogeny was inferred based on the LSU rDNA (D1-D3) and ITS rDNA sequences using maximum likelihood and Bayesian inference. Both O. cf. ovata and O. siamensis, albeit morphologically closely related, can be distinguished by a feature of the thecal pores with pronounced ridges in the latter. Molecular data further supported their species identity. Toxin production in the strains was examined by LC-MS/MS. O. cf. ovata strain T5PRBost02 was observed to produce Ovatoxin-k and Ovatoxin-j2 only; while Ostreocin-B and Ostreocin-D was produced by O. siamensis strain T10PRBost04. This is the first report confirming the production of palytoxins analogs in Ostreopsis species from the region.