Metacaligus latus n. sp. (Copepoda, Caligidae) is described from specimens found parasitic in the oral and gill cavities of the cutlassfish, Trichiurus lepturus Linnaeus, caught from the Strait of Taiwan and landed at Dong-Shih Fishing Port in Chiayi County, Taiwan. It is close to M. uruguayensis (Thomsen, 1949), but can be distinguished from the latter by the possession of shorter caudal rami in both sexes and wider cephalothorax and genital complex in the male. Cladistic (phylogenetic) analysis of the Family Caligidae, based on 23 selected morphological characters, revealed that Metacaligus Thomsen, 1949 is distantly related to Caligus Müller, 1758. It is a valid genus and occurs in sister-group relationship with Apogonia Cressey and Cressey, 1990.