The systematic position of Urotrema Braun, 1900 and the family Urotrematidae Poche, 1926 have always been controversial. Due to its unusual morphological characteristics, lack of knowledge of the life cycle or details of its excretory system, this family was placed within different higher taxonomic groups of digeneans. Despite being one of the most enigmatic digenean families in terms of its phylogenetic affinities, DNA sequence data for Urotrematidae were lacking. Here, we evaluate the phylogenetic relationships of Urotrema using newly obtained partial sequences of the 28S rRNA gene from Urotrema specimens collected in North, Central and South America including the type species U. scabridum Braun, 1900, as well as previously published sequences of digeneans. Our study has demonstrated that Urotrema is phylogenetically closest (100% branch support) to members of Parabascus Looss, 1907 belonging to the family Pleurogenidae Looss, 1899. Thus, the family Urotrematidae becomes a junior synonym of the Pleurogenidae. Urotrema forms a 100% supported clade among the Pleurogenidae, parasitic in warm-blooded vertebrates. However, the phylogenetic relationships and exact systematic position of the remaining 3 genera currently placed in the Urotrematidae remains unclear and requires additional studies as their allocation is mostly based on the terminal posterior position of the genital pore and cirrus-sac. According to our results the genus Parabascus appears to be paraphyletic and requires further detailed phylogenetic and morphological analyses.