Gyrodactylus eyipayipi sp. n. is described from the skin, gills, flute and male brood pouch of captive specimens of the greater pipefish Syngnathus acus L., collected for and maintained at the Two Oceans Aquarium in Cape Town, South Africa. It is the first marine Gyrodactylus species reported from the African continent. The new species is compared to the three known Gyrodactylus species affecting syngnathiform hosts (G. pisculentus Williams, Kritsky, Dunnigan, Lash et Klein, 2008, G. shorti Holliman, 1963, and G. syngnathi Appleby, 1996). Although all four species have similar-sized and shaped attachment hooks with some overlap, separation of the species is possible using marginal hook morphology. The marginal hooks of G. eyipayipi measure (mean) 30 µm in total length and are larger than those of the three other species (mean, 24-28 µm). Gyrodactylus eyipayipi can also be discriminated based on differences in the shape of the marginal hook sickle notably by its long sickle point which extends far beyond the toe, its blunt rounded toe and, by the approximate rectangular shape to the base of the sickle. By comparison, the sloping toe regions of G. pisculentus and G. syngnathi give the sickle bases an approximately triangular shape, whilst the short sickle point and open aperture to the sickles of G. shorti allow for their discrimination from G. eyipayipi.