The armoured dinoflagellateAlexandriumcan be found throughout many of the world’s temperate and tropical marine environments. The genus has been studied extensively since approximately half of its members produce a family of potent neurotoxins, collectively called saxitoxin. These compounds represent a significant threat to animal and environmental health. Moreover, the consumption of bivalve molluscs contaminated with saxitoxin poses a threat to human health. The identification ofAlexandriumcells collected from sea water samples using light microscopy can provide early warnings of a toxic event, giving harvesters and competent authorities time to implement measures that safeguard consumers. However, this method cannot reliably resolveAlexandriumto a species level and, therefore, is unable to differentiate between toxic and non-toxic variants. The assay outlined in this study uses a quick recombinase polymerase amplification and nanopore sequencing method to first target and amplify a 500 bp fragment of the ribosomal RNA large subunit and then sequence the amplicon so that individual species from theAlexandriumgenus can be resolved. The analytical sensitivity and specificity of the assay was assessed using seawater samples spiked with differentAlexandriumspecies. When using a 0.22 µm membrane to capture and resuspend cells, the assay was consistently able to identify a single cell ofA. minutumin 50 mL of seawater. Phylogenetic analysis showed the assay could identify theA. catenella,A. minutum,A. tamutum,A. tamarense,A. pacificum, andA. ostenfeldiispecies from environmental samples, with just the alignment of the reads being sufficient to provide accurate, real-time species identification. By using sequencing data to qualify when the toxicA. catenellaspecies was present, it was possible to improve the correlation between cell counts and shellfish toxicity from r = 0.386 to r = 0.769 (p≤ 0.05). Furthermore, a McNemar’s paired test performed on qualitative data highlighted no statistical differences between samples confirmed positive or negative for toxic species ofAlexandriumby both phylogenetic analysis and real time alignment with the presence or absence of toxins in shellfish. The assay was designed to be deployed in the field for the purposes of in situ testing, which required the development of custom tools and state-of-the-art automation. The assay is rapid and resilient to matrix inhibition, making it suitable as a potential alternative detection method or a complementary one, especially when applying regulatory controls.