Molecular probes were developed for the dinoflagellate genus Azadinium to discriminate among three taxa difficult to differentiate by light microscopy. This genus contains azaspiracid toxin-producing Azadinium spinosum, but also non-toxigenic species. Quantitative polymerase chain reaction (qPCR) and fluorescence in situ hybridization (FISH) assays were applied to cultured isolates and Azadiniumspiked field plankton. Molecular methods were highly specific and sensitive in the unambiguous detection of Azadinium, and thus are valuable for routine plankton, biogeographic and phylogenetic investigations.