The taxonomy and ecology of ostracods in the Caribbean remain incomplete, even though they are among the most successful and ubiquitous microcrustaceans of marine ecosystems. In an effort to enhance our knowledge of the biodiversity, abundance, and distribution of benthic ostracods, several sediment samples were collected from mesophotic coral ecosystems (MCEs) of Puerto Rico and U.S. Virgin Islands at different depths (30–102 m) using technical diving. The highest densities of ostracods were found in the deepest samples (≥61 m), and these were the most abundant and diverse assemblages. All ostracods collected belong to the subclasses Myodocopa Sars and Podocopa Sars. Myodocopa was represented by the families Cypridinidae Baird, Polycopidae Sars, Sarsiellidae Brady & Norman, Rutidermatidae Brady & Norman, Cylindroleberididae Müller, and Philomedidae Müller. On the other hand, Podocopa was represented by the following families: Bairdiidae Sars, Pontocyprididae Müller, Candonidae Kaufmann (subfamily Paracypridinae Sars), Macrocyprididae Müller, Loxoconchidae Sars, Xestoleberididae Sars, Cytherellidae Sars and Cytheromatidae Elofson. The subclass Podocopa showed the highest number of individuals and species. There was a ~100 % correspondence between morphologically identified species and genetically defined species through a short region of the nuclear large subunit ribosomal DNA, which was shown to be appropriate for species recognition and discrimination in ostracods. Using a morphological (shell shape and ornamentation) and molecular barcoding approach (28S rDNA), we provide the first report of the biodiversity of ostracods in the mesophotic coral ecosystems of northeastern Caribbean.