The freshwater fish digenean Pseudosellacotyla lutzi (Freitas, 1941) Yamaguti, 1954 has had an unsettled taxonomic history, and has at various times been classified as a member of Nanophyetidae, Heterophyidae, Microphallidae, Faustulidae, and Cryptogonimidae. Nine individual specimens of the trahira, Hoplias malabaricus (Bloch, 1794), were sampled in the Paraná River basin, Paraná State, Brazil; 22 specimens of P. lutzi were collected. One specimen of P. lutzi was used to obtain a sequence of the domains D1–D3 of the 28S rRNA gene, and to perform a phylogenetic analysis to assess their position and classification within Plagiorchiida. The resulting tree unequivocally shows that the species, along with acanthostomines, belong to the Cryptogonimidae, corroborating recent findings based on the morphology of the cercariae, and in the characteristics of the life cycle. In addition, the study of the ultrastructure of the tegumental spines through scanning electron microscopy allowed us to characterize them as pectinate spines possessing 3 to 8 digitiform projections at their distal end and extending from the anterior to the posterior extremity of the body. This study also provides the first molecular data for a cryptogonimid from South America.