Species of genus Clavellotis (Castro-Romero & Baeza-Kuroki,) are parasites of marine fishes across the world. During the course of a survey on the metazoan parasites of marine fish across the Yucatán Peninsula, Mexico, specimens of a lerneapodid copepod consistent with the concept of Clavelotis were collected from the gills of three species of sparids, and were described as a new species using morphological and molecular characters. Clavellotis mayae n. sp. represents the second species of the genus reported in Mexican coastal waters. The new species morphologically resembles C. dubius and C. sebastidis in the trunk shape but can be readily distinguished by having a short maxilla which is separated to its distal end, a sub-oval and conspicuously larger aliform process, and a distal margin of the trunk bearing pronounced subcircular flaps covering the attachment sites of the egg sacs. The new species further differs from all other known congeners by having a short genital process and mandibles without secondary dentition. Molecular analyses through 28S rDNA and cox1 sequences further corroborate all these morphological distinctions and support the taxonomic placement of the new species within Clavellotis. The relationships of this species with other congeners are discussed in light of molecular evidence.