Mesophotic coral reefs are largely unexplored nearshore habitats. We present illustrations of both sexes of a new copepod species of the family Longipediidae Sars, 1903 collected via scuba-diving with tri-mix rebreathers from mesophotic coral reefs in Puerto Rico as an example of the rich fauna encountered in these habitats. The new species, Longipedia gonzalezi, displays a conservative morphology that characterizes the genus by having a robust body, first pedigers fused to the cephalosome, P4 exp-2 with only 1 medial seta, number of enp-1 medial setae of P1–P4 = 1:1:1:1, number of enp-2 medial setae of P1–P4 = 1:1:2:1, and caudal rami of cylindrical shape about twice as long as wide. The new species belongs to the helgolandica species-group and is morphologically similar to L. helgolandica and L. americana. Species distinction within the genus Longipedia based on morphological characters is challenging because of the conservative morphology of the genus, so we provide the first DNA sequences (28S gene) for future comparisons within the genus. The phylogenetic position of the Polyarthra (a taxon consisting of the families Longipediidae and Canuellidae, whose affinities with Harpacticoida have been questioned) is discussed within Copepoda and other Crustacea. The 28S DNA analysis confirms that Polyarthra are very closely related and are included in the strongly supported Copepoda clade. Polyarthra were not found within the Harpacticoida, which, therefore, remained not as a monophyletic, but as a paraphyletic taxon. Therefore, our 28S data indicate that the claim by Dahms and previous authors for the exclusion of Polyarthra from the Harpacticoida may be valid, and warrants further investigation.