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Paralytic shellfish poisoning (PSP) is a major human health issue that occurs worldwide. Species of the marine dinoflagellate genus Alexandrium can produce dangerous amounts of paralytic shellfish toxins responsible for PSP poisoning at extremely low cell densities. Current detection and identification methods for Alexandrium typically used by coastal managers are time-consuming, expensive, require special training, and are typically unable to distinguish between toxin-producing and non toxin-producing species. Therefore, there is a need for new methods to address these issues. We have developed a field-deployable method that uses surface plasmon resonance (SPR) and species-specific peptide nucleic acid probes to detect Alexandrium rRNA. This instrument has been tested using synthetic nucleotide sequences and validated against the industry-standard Biacore SPR instrument. This instrument can reliably discriminate between synthetic nucleotide sequences designed to mimic two species of Alexandrium found to co-occur in the Gulf of Maine, and also has a higher sensitivity to low nucleotide concentrations than the Biacore instrument.