Infection by the protozoan parasite Toxoplasma gondii, is widespread in humans and many other warm-blooded animals. More than half billion of world human population has serum antibodies to T. gondii and Sheep and goats are more widely infected with T. gondii. T. gondii infection can be diagnosed indirectly with serological methods and directly by polymerase chain reaction (PCR), hybridization, isolation and histology. A total number of 124 goats and 113 sheep blood samples were collected from Urmia region and PCR was used for detection of the pathogenic protozoan T. gondii using B1 gene. The targeted B1 gene is highly conserved in all T. gondii strains and is multiple copy genes whit in the T. gondii genome. The method used for the characterization of T. gondii strains implied digestion with AluI restriction enzyme of the fragments amplified. The results indicated three positive sheep (1.26%) with one RFLP patterns. The results indicated that the same strain of T. gondii has infected sheep in the region.