The present study aims to describe a new genus and species of microphalloid digenean parasite of two species of bats of the genus Peropteryx from the Mexican Neotropics (in the states of Chiapas and Yucatán). Morphological and molecular data (28s rDNA ribosomal gene sequences) were used to study Digeneans. Sagittatrema zutzi gen. nov. sp., nov., is diagnosed morphologically by having a sagittiform body, a genital pore in the midline of the body, posterior to the ventral sucker, and a cirrus sac running through much of the diameter of the ventral sucker. The nine sequences generated from the 28S rDNA gene were used to examine the phylogenetic affinities of this new taxon within the superfamily Microphalloidea Ward, 1901, using Maximum Likelihood and Bayesian Inference analyses. Both analyses resulted in trees with similar topologies and formed a well-supported clade (Bt = 100; pp = 1) with the Sagittatrema sequences. Because of the new genus’s phylogenetic position and that some sister families to the proposed taxa, like Pleurogenidae and Prosthogonimidae, are polyphyletic, we prefer to consider Sagittatrema as a genus incertae sedis within Microphalloidea. A full systematic review of microphalloids is needed to confirm their phylogenetic position.