Introduction Lophomoniasis is caused by Lophomonas spp., a new emerging protozoan, which commonly affects the human lower respiratory tract. The Lophomonas parasite mostly lives commensally in the hindgut of cockroaches. Case Presentation We present the case of a 33-year-old woman, 30 weeks pregnant, who had severe COVID-19. She was intubated upon admission and began the routine COVID-19 treatment. To rule out possible super infection dual with COVID-19, microscopic examination of the patient's mini-bronchoalveolar lavage (mini-BAL) specimen, revealed L. blattarum, which was identified by the SSU rRNA-PCR and sequencing approaches (accession number: MZ093069). According to that, the patient was treated successfully with metronidazole. Conclusion To prevent serious complications, lophomoniasis should be listed in co-morbidity cases of COVID-19 infection during the COVID-19 pandemic worldwide. To the best of our knowledge, this is the first co-infection of Lophomonas blattarum and COVID-19 in the world which has been confirmed using a molecular approach.