Morphology and phylogenetic position of the marine harmful raphidophyte Chattonella isolated from Bolinao, Pangasinan, Philippines in 2013 and 2017 were examined using light microscopy and molecular phylogeny inferred from LSU rDNA and ITS sequences. Cells of Chattonella were variable in shape and typically teardropshaped with a roundish antapical end, 26.0–49.5 μm in length, with an anterior flagellum directing swimming direction and a posterior flagellum trailing backward. Cell surface was covered by numerous small granules and several larger button-like rounded bodies. Discharge of transparent tubular mucocysts was also observed from cells just before collapse. Numerous brownish chloroplasts were located peripherally, each with a pyrenoid. Two Chattonella strains isolated in 2017 had identical LSU rDNA and ITS sequences and branched in the clade of Chattonella subsalsa, and were closely related especially to strains isolated from the Gulf of Mexico and East coast of USA. This is the first report of C. subsalsa based on morphological and phylogenetic information from the Philippines.