Probes that are specific for the two dinoflagellate species, Alexandriutrl catene/la and A. tamarense, were designed based on their known sequence of D1-D2 region of the large-subunit ribosomal RNA gene (28S rDNA). The probes were applied to test against two straints of Ale.xandrium. The first strain t, Alexandrium 2.1, was isolated from coastal waters of Vietnam, having morphological characteristics fit the description of A. tamarense. The second straint, Alexandrium 2.7, was collected from Japanese coastline has morphology falls into the description of A. catenella. Result showed that the probes are very high specific. They only positive (light green in wavelength 490nm) for the A. catenella and absolutely no positive with any other species in nature, even their closest related species. This method appears to be very useful for rapid identification of algal species.