Copepods of the genus Cletocamptus are common inhabitants of coastal saline lagoons of the greater Caribbean. They are abundant in southern Puerto Rico, where past studies indicate the presence of one species, Cletocamptus dominicanus; but genetic and ecological studies have yet to be conducted. For a year, we surveyed the Cletocamptus populations of three lagoons (Candelaria, Fraternidad, and Playa Sucia) in southwestern Puerto Rico. Densities fluctuated within and between lagoons, suggesting patchy distribution. Their average density per lagoon ranged from 0 to 608 copepods/cm² of sediment. Salinity, temperature, and pH were not correlated with copepod densities, suggesting tolerance to environmental fluctuations. Specimens exhibited morphological variability, motivating us to assess the standing genetic variability and the potential of cryptic species by employing two molecular markers. The mitochondrial COI and the nuclear ribosomal 28S genes were sequenced from 130 and 118 specimens, respectively, collected from Candelaria, Fraternidad, and Playa Sucia, as well as from an additional four lagoons (Petrona, Encarnación, Providencia, and Flamenco). Phylogenetic analyses using both genes indicate the presence of at least four lineages. Based on COI sequences, corrected sequence divergence between the lineages ranged from 13% to 43%. Given the large sequence divergence among the Cletocamptus lineages, we used single-locus species delimitation tools (GMYC, bPTP, mPTP, ASAP, and ABGD) to assess for the presence of additional species beyond the previously reported C. dominicanus. Most delimitation tests grouped taxa into five putative species. Cletocamptus spp. are often the numerically dominant benthic metazoans in these important coastal habitats and warrant taxonomic, genomic, and physiological studies to understand their divergence and adaptations to this unique environment.