BACKGROUND Toxoplasma gondii is an obligate, intracellular protozoon that develops its sexual stage in cat's intestinal epithelial cells as definitive host and develops its asexual stage in different tissues of a wide range hosts called intermediate host. The protozoon is a food-borne and worldwide parasite that can cause serious complications such as abortion in pregnant women, encephalitis, and ocular toxoplasmosis. The present study aimed to genotype T. gondii strains isolated from patients with toxoplasmic retinochoroiditis. METHODS Fifty-two blood samples were taken from patients with ocular toxoplasmosis, from July 2013 to July 2014. The specimens were collected from three ophthalmological hospitals of Tehran, Iran. After that, DNA extraction was performed using kit on separated buffy coats of serologically positive blood samples. Then PCR was done in GRA6 gene. For digestion of products, MseI endonuclease was used. Finally, some of the PCR products were sequenced. RESULTS All of 52 samples were found positive by serological and PCR-RFLP methods and all of isolated strains belong to type III genotype. Type III genotype has the highest prevalence in Iranian ocular toxoplasmic patients. CONCLUSIONS T. gondii, particularly its type III should not be neglected as a cause of retinochoroiditis.