Harmful algal blooms represent a major threat to marine production, and particularly to shellfish farming. Alexandrium minutum, which causes paralytic shellfish poisoning, is occurring with increasing frequency along European coasts. Current regulatory methods to analyze environmental samples are tedious and time consuming because they require taxonomists and involve animal experiments. New rapid detection methods, such as immunoassays, are needed to ensure a fast alert system and for field studies of algal ecodynamics. Rat monoclonal antibodies were raised and selected for their ability to specifically recognize a surface antigen for the A. minutum strain AM89BM from the Bay of Morlaix, France. A whole-cell ELISA was designed, leading to the selection of one AMI6 mAb that was selected for its performance in a large set of immunochemical formats. Moreover, AMI6 mAb displayed no detectable cross-reactivity with most algae found in similar biotopes, particularly those which might be mistaken during a conventional light microscope counting Heterocapsa triquetra, Scrippsiella trochoidea, Karenia mikimotoi, and two strains of Alexandrium tamarense, either toxic or not. Using colloidal gold conjugates on immunodecorated cells, we used electron microscopy to show that AMI6 mAb targets an exposed antigen at the surface of A. minutum. It was noted that this antibody could work with many preparations of A. minutum cells, i.e. fresh, frozen or dried cells. The detection limit in the whole-cell ELISA was found to be 10 cells per well. This assay displayed sensitivity and specificity when used for the analysis of natural seawater samples. A large set of immunochemical formats, using either AMI6 mAb or related antibodies from this series, could be further envisaged for designing environmental biosensors.