Species specific primers for PCR were constructed for two harmful species of dinoflagellates, Gymnodinium mikimotoi and Alexandrium minutum. The primers amplified a product of expected size from cultured cells of G. mikimotoi and A. minutum but did not yield any product with a wide range of other cultured algal cells, used as negative controls. The confirmation of PCR products was performed by restriction enzyme digestion of the products. The PCR method for detection of G. mikimotoi and A. minutum was applied on field samples. G. mikimotoi could be detected in 11 field samples by microscopy and all these field samples were positive by PCR. The cell counts of G. mikimotoi in the samples ranged from 306-2077 l-1. A. minutum could be detected by microscopy in three different field samples which had cell counts ranging from 115 -1115 cells l-1. A. minutum was detected by PCR from two of these field samples, but the sample which had a cell count of 115 l-1 A. minutum cells did not yield any product by PCR. Plankton samples that were negative by microscopy for any of the two species, were also negative by PCR. All the PCR products from field samples were confirmed by restriction enzyme digestion.