The intestinal microbiota has become the center of attention, not only in microbiology but also in all fields of medicine. There has been an intense activity in studies that investigate the composition and function of the intestinal microbiota. The imbalance in the diversity of bacteria that constitute microbiota has been defined as "dysbiosis" and associated with various diseases. Blastocystis spp. is a eukaryotic protist and the most prevalent protozoan of the human gastrointestinal system. The frequency of observed colonization of Blastocystis spp. in asymptomatic cases has made its association with diseases controversial. It was found in some studies that there is a positive correlation between Blastocystis and the bacterial diversity of the intestinal microbiota. This implies that the parasite may play a role in intestinal homeostasis. Human and animal studies on this subject play an important role in understanding this relationship.