Pentatrichomonas hominis and Tritrichomonas foetus (cat genotype) have been commonly identified as intestinal trichomonads in both dogs and cats. Although P. hominis is considered as non-pathogenic protozoa in many kinds of mammals, it has the potential for zoonotic transmission. T. foetus has been recognized as the emerging causative agent of diarrhea in cats without the risk of zoonotic transmission. As pet shops are the major source of young companion animals, the present study discusses the molecular prevalence of P. hominis and T. foetus from 544 pet shop puppies and 409 kittens. The results suggest that the prevalence of P. hominis (puppies: 7.0%; kittens: 0.5%) and T. foetus (puppies: 0%; kittens: 2.4%) in pet shop young animals are low. In addition, the infections of P. hominis and T. foetus are not always associated with the clinical signs (soft or diarrhea feces).