Six families belonging to the Paramphistomoidea superfamily have been reported in South America, with only Zonocotylidae and Balanorchiidae being endemic. The Zonocotylidae was initially classified as Aspidogastrea and then as a paramphistomoid. This family comprises a single genus, Zononocotyle, with two species. It is primarily characterized by having an attachment organ with transverse ridges and a single testis. The placement of Zonocotylidae within Paramphistomoidea is controversial, as some researchers speculate that this genus is the most primitive member of the superfamily, while others consider it an aberrant form. The main objectives of our study were to provide the first sequences of Zonocotylidae and elucidate its phylogenetic position. We amplified the 28S gene from two parasites from Cyphocharax sp. from Punta Lara, Buenos Aires. Newly generated sequences were used to infer the phylogenetic relationships with other Paramphistomoidea species using a Bayesian approach. Zonocotylidae were clustered with Dadayiinae and Kalitrematinae (Cladorchiidae) species found in freshwater fishes from South America. Genetic analyses revealed that they formed a well-supported clade with cladorchiids in freshwater hosts from South America. However, the occurrence of genera of Cladorchiidae in North America, Middle America, Asia, and Australia suggested its polyphyletic nature and may indicate the need for the erection of new families. Other Paramphistomoidea families may also require further revision. The addition of new sequences to phylogenetic analyses along with a comprehensive and more detailed description of the genera will help resolve the relationships within this group.