A total of 12 adult cestodes were collected from the bile ducts of domestic mice (Mus musculus) from Lima, Peru. Various features of the scolex and mature proglottids of the tapeworms were observed for morphological identification. A molecular diagnosis was performed by PCR-based partial sequencing of mitochondrial gene of cytochrome c oxidase subunit 1 (cox1). All cestodes were identified as Hymenolepis microstoma by morphology and molecular methods. The H. microstoma isolate from Peru showed significant sequence similarity with previously reported isolates of H. microstoma (>99%). Our report confirms the presence of the parasite in mice from Lima.