About 30 benthic Prorocentrum species have been described, some of which producing okadaic acid and derivatives involved in diarrhetic shellfish poisoning. The western Caribbean has been extensively studied for benthic dinoflagellates associated with ciguatera, and fifteen Prorocentrum species were described from mangroves and coral reefs of Belize. In contrast, no study reported the diversity of this genus in the Eastern Caribbean, especially in the Lesser Antilles. This study adds to the biodiversity knowledge in Martinique Island by investigating one site of the Caribbean coast from 2010 to 2017. Sediment samples were collected each year in March and studied taxonomically. Identification was realized morphologically by scanning electron microscopy, while the partial large subunit (LSU) ribosomal DNA was sequenced for 42 isolated specimens (single-cells) and one strain in culture. A molecular phylogenetic analysis revealed 11 OTUs from Martinique, identified morphologically as P. concavum, P. cf. foraminosum, P. cf. tropicale, P. lima, P. hoffmannianum, P. cf. norrisianum, P. glenanicum, P. panamense, P. cf. sculptile, P. cf. fukuyoi, and P. rhathymum. Two morphospecies were also identified (P. cf. maculosum and P. cf. ruetzlerianum) but with no sequence obtained. Some species like P. cf. tropicale and P. cf. norrisinamum are sequenced for the first time. Our analysis reveals probable former misidentifications of P. cf. foraminosum and P. cf. sculptile since the sequences from Martinique form new clades and their geographical origin are closer from the type locality than any other previous studies. Further studies and sequences from the type localities are yet required to assess identifications.