Blastocystis sp. is more prevalent in mentally-retarded individuals, immunocompromised patients, and organ recipients. There are no inclusive studies in Iran evaluating the prevalence and molecular identification of Blastocystis sp. infection in schizophrenic patients. This study aimed to determine prevalence and subtype distribution of Blastocystis sp. in schizophrenic patients in Tehran province, Iran. This cross-sectional study was performed on 58 stool samples of schizophrenic male patients in Tehran province, Iran, using the sequence-tagged site (STS) and ST-specific primers. Overall, 58 stool samples were collected from hospitalized male patients with schizophrenia in Tehran province. After conventional PCR, positive samples were probed by ST-specific and STS primers. Following molecular evaluation, 32 samples (55.2%) were positive for Blastocystis sp. Which, 28 (87.5%) cases were ST3, 3 (9.4%) cases were found to be ST9, and one case (3.1%) was ST1.This study was the first report of the ST9 of Blastocystis in Iran. Blastocystis infection was more prevalent in asymptomatic patients (55.6%) compared with symptomatic patients (55%). There was a significant association between the duration of hospitalization and Blastocystis infection rate (0.002). The results of the present study represented a high prevalence and significance of Blastocystis sp. infection in schizophrenic patients. Patients with schizophrenia are unable to attend to their own care. Also, schizophrenic patients have a lack of perception that can result in poor hygiene, which needs more care, accuracy, prevention, and control.