Goodea atripinnis Jordan, 1880 has a broad range of habitats and is the most widespread species of the endemic goodeid fishes, which inhabit the central highlands of Mexico. This species is known to be host to a high diversity of helminth parasites from which only three belong to the genus Gyrodactylus von Nordmann, 1832: G. lamothei Mendoza-Palmero, Sereno-Uribe et Salgado-Maldonado, 2009, G. mexicanus Mendoza-Palmero, Sereno-Uribe et Salgado-Maldonado, 2009, and G. tomahuac Rubio-Godoy, Razo-Mendivil, García-Vásquez, Freeman, Shinn et Paladini, 2016. Here, we describe three new species of Gyrodactylus collected from G. atripinnis, which were characterised morphologically (sclerites of the attachment apparatus) and molecularly (sequences of the internal transcribed spacer region of the rDNA): Gyrodactylus iunuri n. sp., Gyrodactylus katamba n. sp. and Gyrodactylus tepari n. sp. These new species were collected in three different states in the Mexican Highlands: Guanajuato, Jalisco and Querétaro. Both morphological and molecular data support the hypothesis that two distinct groups of gyrodactylids infect goodeid fishes: G. iunuri n. sp., G. tepari n. sp. and G. tomahuac possess robust hamuli and are closely related phylogenetically; while G. katamba n. sp. resembles G. lamothei in having slender hamuli with accessory sclerites adjacent to the hamuli root, and apparently shares a common ancestor with gyrodactylids infecting poeciliid fishes. New locality records of G. tomahuac are presented. The addition of the three new species of Gyrodactylus as parasites of G. atripinnis makes monogeneans the second most abundant parasite group known to infect this host.