In the present report metacestodes were collected from the mesentery of a taruca (Hippocamelus antisensis) and from the omentum of a red brocket deer (Mazama americana) in Peru. Various metacestodes parameters, including rostellar hook characteristics, were measured. Molecular analysis was performed to amplify the mitochondrial cytochrome c oxidase subunit 1 gene from metacestode isolates. Metacestodes were identified as T. hydatigena by morphology and molecular methods. This constitutes the first molecular detection of T. hydatigena metacestodes in the taruca and the red brocket deer and demonstrates that these animal species are natural intermediate hosts for this parasite.