It has been known that several species of Pseudo-nitzschia produce a toxin, domoic acid (DA), responsible for the syndrome commonly referred to as amnestic shellfish poisoning (ASP), and then make a serious impact on shellfish farm in several countries. There have been no reports on risk assessments of DA contamination of shellfish in Korea. However, recently, we have observed potentially toxic P. multiseries and non-toxic P. pungens using scanning electron microscope, which are very similar morphologically and are considerable confusion under the photomicroscope. It is therefore desirable to detect and enumerate such species for harmful algae monitoring and prediction systems. In this study, we applied DNA probes and fluorescent tagged lectins to differentiate toxic P. multiseries from non-toxic P. pungens isolated from Chinhae Bay. From the binding activity of lectins, two species were responsible for bright fluorescence on the cell surface of ConA and RCA, whereas PNA, UEA and DBA presented no fluorescence with P. multiseries and P. pungens. In particular, fluorescent WGA specifically bound with P. multiseries but not with P. pungens, indicating a desirable method of rapid and easy discrimination between tested Pseudo-nitzschia species. In addition, we have tested species-specific oligonucleotide DNA probes to these two species with the aid of whole cell hybridization by filter tube system. The positive control (uniC) probe bound to both Pseudo-nitzschia species, but negative control (uniR) and Alexandrium tamarense (NA1) probes did not bind to both species. However, P. multiseries DNA probe (muD1) was negative for P. pungens under the epifluorescent microscope, suggesting that these organisms were recognized by their own specific oligonucleotide probes and distinguished between positive and negative control probe. Thus this technique is suitable to differentiate toxic P. multiseries from non-toxic P. pungens for a specific fragment of rRNA.