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Two new species, Encotyllabe cheilodactyli and Encotyllabe antofagastensis (Monogenea: Capsalidae), have been found in the pharyngeal plates of Cheilodactylus variegatus and Anisotremus scapularis, respectively, in northern Chile (23°38′N, 70°24′W). Descriptions of the new species were based on morphometric and molecular evidence. Both species differ from previously described species of the genus by a combination of characteristics, including the size and relative position of the testes and the shapes of the major and small hamulus. In addition, E. cheilodactyli is unique among the known species of Encotyllabe due to the testes crossing the equatorial line of the body proper, and E. antofagastensis is unique among the known species of Encotyllabe due to its penis structure and anatomy leading to the genital pore. The analysis of the cytochrome c oxidase I gene as well as morphometric analyses demonstrated that the specimens belonged to 2 different species.