IntroductionA new species of the genus Caligus is described based on specimens collected from pompano, Trachinotus ovatus (Linnaeus), caught in eastern Atlantic waters, near the Madeira archipelago.MethodsPompano (n = 21) were purchased from the local fish market and examined for parasitic copepods. Morphological features of the copepods were examined and drawn using an Olympus BX51 equipped with a drawing tube. Key diagnostic characters were scanned using a confocal laser scanning microscope and a scanning electron microscope.ResultsCaligus madeirensis sp. nov., can be distinguished from all congeners (270 spp.) by the combination of the following characters: (i) an accessory process on the 3 outer terminal spines located on the distal exopodal segment of leg 1, (ii) a mandible with 14 teeth, (iii) a sternal furca with parallel, spatulate tines, (iv) a maxilliped with 2 simple setae at base of a claw, (v) a leg 3 with second endopodal segment with 5 pinnate setae, (vi) a 2-segmented leg 4 exopod with I; III spine formula, (vii) a male antenna with 4 overlapping plates on the distal segment, (viii) a male maxilliped corpus bearing a prominent myxal process ornamented with dense corrugations along inner margin.ConclusionTogether with Caligus madeirensis sp. nov., the Caligus fauna of Portugal consists of 13 species reported from 17 Portuguese marine fishes. Considering the large number of marine fish species (510 spp.) currently recorded from Portuguese waters it seems that only 3.3% of the Portuguese marine fishes have been found to be infested with species of the genus Caligus O.F. Müller, 1758, the result of which, however, might be due to limited sampling.Electronic supplementary materialThe online version of this article (10.1007/s11686-020-00290-3) contains supplementary material, which is available to authorized users.