The first molecular assessment of phylogenetic relationships of cladorchiid digeneans (superfamily Paramphistomoidea Fischoeder, 1901) from freshwater fishes based on 28S rDNA, ITS2 and cox1 sequences reveals the subfamilies Dadayiinae Fukui, 1929 and Kalitrematinae Travassos, 1933 as non-monophyletic, whereas Dadaytrema Travassos, 1931 represented by three species is monophyletic. Fourteen species of cladorchiids were found in characiform, perciform and siluriform fishes in the Neotropical Region (Brazil and Peru), with numerous new host and geographical records. The first scanning electron micrographs of seven species are presented. Two new species of dadayiine and one new species of kalitrematine paramphistomes are described. Microrchis macrovarium sp. n. from Pimelodella cristata (Müller et Troschel) (type host), Tetranematichthys quadrifilis (Kner) and Pterodoras granulosus (Valenciennes) in Brazil and Peru differs from all three congeners in that the testes are directly tandem, not oblique, and that the ovary, between the caecal ends, is widely separated from the testes. Pronamphistoma philippei sp. n. from Heros sp. in Brazil is distinguished from the type and only species, Pronamphistoma cichlasomae Thatcher, 1992, by the absence of the anterior collar-like expansion present in the type species, the presence of extramural rather than intramural pharyngeal sacs, and the unusual development of the dorsal and ventral exterior circular muscle fibre series in the acetabulum. Pseudocladorchis romani sp. n. from P. granulosus (type host), Brachyplatystoma vaillantii (Valenciennes), Calophysus macropterus (Lichtenstein), Megalodoras uranoscopus (Eigenmann et Eigenmann) and Oxydoras niger (Valenciennes) in Brazil and Peru, is most similar to Pseudocladorchis nephrodorchis Daday, 1907 but differs in the shape of the testes (irregular, versus reniform in the latter species) and the size of the ovary (as large as, or larger than, the testes in the new species). The generic diagnosis of Pronamphistoma Thatcher, 1992 is amended. Dadaytremoides parauchenipteri Lunaschi, 1989 is transferred to Doradamphistoma Thatcher, 1979 as D. parauchenipteri (Lunaschi, 1989) comb. n. based on morphological and molecular evidence.
Keywords: 28S rDNA; Characiformes; Cichlidae; ITS2; SEM; Siluriformes; South America; Trematoda; cox1; diversity; new species; taxonomy.