Various species of toxic dinoflagellates have been isolated from various sites in the Philippines. In this study, we characterized a number of these isolates using a molecular approach and Confocal Laser Scanning Microscopy (CLSM). Phylogenetic analysis using genetic markers (LSU rDNA, SSU rDNA, and cytochrome oxidase b) confirmed the identity of the isolates as Pyrodinium bahamense var. compressum, Alexandrium affine, Gymnodinium catenatum, Prorocentrum sigmoides, P. micans and P. rhathymum. Morphological differences among strains of Pyrodinium were very minor and could not be readily correlated with geographical variation. Intra-species polymorphism in the form of single nucleotide polymorphisms (SNPs) and deletions/insertions in the sequences were also observed. However, in general, the SNPs in these markers are too few and may not provide sufficient resolution to allow these markers to be used for population genetic studies.