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Knowledge on the diversity of parasitic flatworms of Western Mediterranean cyprinids is extremely scarce. In the present study, we parasitologically investigated 12 cyprinid species across the Strait of Gibraltar inhabiting watersheds in northwest Africa (Morocco) and Iberia (Portugal and Spain). Taxonomically relevant features of the attachment organ and sequences of the 18S rDNA and ITS regions were used for species delineation and to investigate their phylogenetic relatedness. Among the <i>Gyrodactylus</i> collected from Morocco and Spain, we identified specimens with an unusual T-shaped dorsal bar observed herein for the first time. In contrast, the membranous patch-like structure surrounding the twisted inner roots of hamuli and the median ridge of the ventral bar have been generally observed in Eurasian relatives. Our analyses suggest vicariant speciation of <i>Gyrodactylus</i> across the Strait of Gibraltar. We describe herein <i>G. gibraltarensis</i> sp. nov. from Iberian <i>Luciobarbus graellsii</i>; <i>G. moroccensis</i> sp. nov. from northwest African cyprinids, i.e., <i>L. maghrebensis</i>, <i>L. rabatensis</i>, <i>L. rifensis</i>, <i>L. yahyaouii</i>, and <i>L. zayanensis</i>; and finally, <i>G. pseudomoroccensis</i> sp. nov. from Moroccan <i>L. ksibi</i>, all possessing a new haptoral configuration. The genetic divergence and conservative morphologies in populations of <i>G. moroccensis</i> sp. nov. from five cyprinid species support its ongoing speciation in Northwest Africa. The West Mediterranean lineage was revealed to be monophyletic, with Eurasian species forming a sister group. Morphologically, West Mediterranean <i>Gyrodactylus</i> also appeared to be of Middle Eastern origin. <i>Gyrodactylus</i> spp. possessing an unusual T-shaped dorsal bar have most likely speciated, allowing for the appearance of a haptoral morphology that is restricted to the region across the Strait of Gibraltar. To conclude, viviparous <i>Gyrodactylus</i> reflect parasite speciation across the Strait of Gibraltar and the historical biogeography of cyprinids in the West Mediterranean.