Dinoflagellates are the important primary producers in aquatic environments. In oceans they play interesting role in ecological functions such as red tide forming organisms symbiont of coral reef or sea anemone and DSP (Diarrhetic Shellfish Poisoning) or PSP (Paralytic Shellfish Poisoning) producing organisms. Morpologhy and molecular analysis of dinoflagellates were conducted on November2002 to March 2003. The phylogenetic studies based on 18S rDNA analyses squence have begun to appear more frequently in the literature as attetion has turned to relationships within the major eukaryotic lineages particular importance for the taxonomy of the aromared and unarmored genera of dinoflagellates (Gyrodinium sp. Cachonina sp. Gymnodinium sp. Amphidinium sp.) because many of the genera cause extensive plankton blooms fish kills and other harmful events were studied used to amplify 18S rDNA present in the total DNA extacted from algal pellet. The amp ify approximately 1400 bp of the nuclear-encoded LSU rDNA gene using terminal primerirs DIR products were cheked by 1.0 % agarose gel electrophoresis then cloning with TA cloning KIT Sequencing were analyzed by the GENETIX Mac Softaware Homology search by Blast and Phylogenetic analysis. Results of hylogenetic analysis of 18S rDNA are Strain no. 10893 (un identified) from the genera it is belonging Gymnodinium or Polarella. Strain no. 10795 is closely related other species Cachonina hallii. We tentatively named strain no 11151 avd 11160 similiar to Gyrodinium or Gymnodinium based on morphology but these strain indepently position in this tree and is not a real of Gymnodinium sensu stricto. It is possible we can aestablish the new genera for strain no. 11151 11160 because this not cluster any other unarmored species.