Benthic dinoflagellates of the genera Coolia, Ostreopsis and Prorocentrum isolated from coastal waters of the south-eastern Bay of Biscay were identified morphologically by means of light microscopy (LM) including epifluorescence microscopy, and scanning electron microscopy (SEM). To identify the strains to species level, molecular phylogenetic analyses using the nuclear large subunit rDNA (LSU) were performed for 16 strains of the three genera. These morphological and phylogenetic analyses revealed the presence of the following species: Coolia canariensis S. Fraga, Coolia monotis Meunier, Ostreopsis cf. siamensis Schmidt, Prorocentrum emarginatun Fukuyo, P. lima (Ehrenberg) Dodge, P. rhathymum Loeblich III, Sherley & Schmidt, and two as yet unidentified species, which in the phylogenetic tree were grouped with different strains of Prorocentrum emarginatun and P. fukuyoi Murray et Nagahama from GenBank. A strain from Minorca (Balearic Islands, western Mediterranean Sea) analysed in this study for comparative purposes and fitting morphologically into the P. emarginatum/P. fukuyoi group also appeared in this cluster, which seems to include morphologically cryptic or semicryptic species. The most common taxa were Coolia monotis, Ostreopsis cf. siamensis and Prorocentrum lima, which appeared at most sampling sites. Only the strains corresponding to Ostreopsis cf. siamensis and Prorocentrum lima were toxic to Artemia franciscana.