Two new species, Choricotyle scapularis and Choricotyle isaciencis (Monogenea: Diclidophoridae), are described from the gills of haemulid fishes, Anisotremus scapularis and Isacia conceptionis, respectively, in San Jorge Bay, northern Chile (23°42′S, 70°24′W); they are compared with the known species in the genus. Diagnostic characters for C. scapularis includes the number of hooks in the male copulatory organ, a developed isthmus, the shape of the haptor, and the number of testes. The diagnostic characters for C. isaciensis include the presence of an oval accesory sclerite in the clamps, the number of testes, the number of hooks in the male copulatory organ, and the relative clamp peduncle size.