FITC‐conjugated lectins proved to be effective probes for differentiating between morphologically similar dinoflagellate species isolated from New Zealand coastal waters. In particular the binding (fluorescence) of peanut (PNA) lectin differentiatedG. mikimotoifromGymnodiniumsp. (Waimangu) andG. pulchellumand the non‐binding ofHelix pomatia(HPA) and wheat germ (WGA) lectins discriminated betweenG. mikimotoiand the otherGymnodiniumspecies tested.G. breve(Florida) was differentiated from the New Zealand isolates by binding with soy bean (SBA) lectin.Ulex europeus(UEA) distinguished the toxic speciesAlexandrium minutumfrom the morphologically similar, but non‐toxic,Cachonina hallii. Two strains ofProrocentrum lima(Spain and Rangaunu) were not differentiated by the lectins, butP. limawas differentiated fromP. compressum.