Since toxic Alexandrium catenella and non-toxic A. fraterculus are morphologically similar, they are difficult to discriminate under the light microscope. However, a novel technology, such as fluorescein isothiocyanate (FITC)-conjugated lectin probes enables easy and rapid differentiation. Toxic A. catenella bound seven different lectins, whereas the non-toxic A. fratercuzus did not bind Arachis hypogaea (PNA) lectin. In addition, Pseudo-nitrschia species in this study were also difficult to identify to species level with light microscope techniques, but it was possible to classify them using fluorescent lectins. Pseudo-nitzschia multistriata, P. subfraudulenta and P. pungens bound Canavalia ensiformis (ConA), whereas P. subpaclfica did not, and P. pungens also bound Ricinus communis (RCA). These results imply that lectin could be used as a critical tool in the differentiation of P. multistriata, P. subfraudulenta and P. pungens. However, P. subpacifica was not differentiated by the lectins tested. Therefore, it isconcluded that lectin probes are useful for discriminating toxic A. catenella from non-toxic A. fraterculus, and for the identification of some Pseudo-nitzschia species. In addition, this method has a great potential to speed and detection between non-toxic and toxic harmful algal blooms (HABs) in Korean biotoxin monitoring systems.