A method of PCR (polymerase chain reaction) and ELISA (enzyme-linked immunosorbent assay) immunoassay for the detection of the toxic Alexandrium species from cultured isolates and field samples of seawater is presented. The PCR-primers targeting the ITS-5.8S rDNA regions specific for the Alexandrium genus, amplified a fragment of approximately 286 bp (base pair) in the 5.8S ribosomal DNA (rDNA) and Internal Transcribed Spacer 1 and 2 (ITS1 and ITS2) regions from the Alexandrium isolates. The solid-fase elisa immunoassay involved application of a biotinylated-labeled primer targeting the ITS-5.8S rDNA regions; the PCR-amplified products, containing the digoxigenin-11-deoxiuracil triphosphate nucleotide (dig-dUTP), were captured on the streptavidin-coated microplate. The captured molecule were hybridized to an anti-digoxigenin antibody conjugated with alkaline phosphatase activity, which served to develop an enzyme-driven colourimetric reaction. The results indicated that the genus-specific biotinylated primer recognized the ITS-5.8S rDNA target sequences of Alexandrium cultured isolates by capturing streptavidin molecules-coated microplate, but did not target rDNA from other closely related groups of microalgae or marine phytoplankton populations of seawater samples, in which the Alexandrium species were absent; furthermore, the number of Alexandrium cells in the samples resulted in a proportional appearance of colour generated by the phosphatase activity in the presence of a chromogenic substrate and measured in a plate reader. The reproducibility and variability of this method were also tested. Thus, the immuno-PCR and ELISA assay is a useful technique to detect the presence of the target microalgal species in cultured and field samples; this method seems to be faster and simple, compared with other identification methods currently in use.