Harmful algal blooms (HABs) pose severe threats to marine ecosystems, aquaculture productivity, and public health worldwide, yet rapid on-site detection for toxigenic species remains technically challenging. Here, we developed a diagnostic assay integrating recombinase polymerase amplification (RPA) with CRISPR/Cas12a and lateral flow dipstick (LFD) for the visual detection of Pseudo-nitzschia multistrata, a  toxigenic diatom species responsible for the production of neurotoxin domoic acid (DA). The assay targets the dabA gene, a functionally critical component of the DA biosynthesis gene cluster, whose detection serves as a molecular proxy for the toxigenic potential of the species. Following a simple alkaline lysis step, the released DNA was subjected to RPA for pre-amplification of the dabA gene at 39℃ for 35 minutes. The RPA product then served as the substrate for CRISPR/Cas12a reactions, in which the Cas12a protein, guide RNA, and a fluorescently labeled ssDNA probe were incubated at 37℃ for 30 min. Cas12a specifically recognized the target amplicon and activated its trans-cleavage activity, resulting in the cleavage of the probe. The RPA-CRISPR products were subsequently applied to LFD strips, with results visually interpreted within 5 min. The entire workflow, from cell lysis to result readout, can be accomplished within 1.5 hours without requiring thermal cycling equipment. This method offers a rapid, equipment-independent, and user-friendly approach for the detection of toxigenic HAB species, providing a technical foundation for early warning and routine monitoring of HAB events in coastal ecosystems.
 

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